Who Makes The Rules?
People tend to be a little mystified by how there is a such a difference between taxable income and reported income, but if you dig into the notes to the financial statements and the statement of cash flows you can usually tease out most of what creates the difference.
The approach that Warren is recommending is intellectually lazy. The law as enacted and enforced (or not enforced) is producing a result that does not seem right. So let’s slap something else on top of it to make sure the companies pay something.
That’s how we ended up getting the AMT back in the day.  Rather than trim and eliminate a variety of exclusions, credits and deductions, a parallel system was created that produced a different tax.  What is different about this proposal is that the parallel system already exists.  It is called Generally Accepted Accounting Principles.
In the United States, the ultimate authority on what is or is not GAAP is the Financial Accounting Standards Board (FASB).  
Established in 1973, the Financial Accounting Standards Board (FASB) is the i ndependent, private-sector, not-for-profit organization based in Norwalk, Connecticut, that establishes financial accounting and reporting standards for public and private companies and not-for-profit organizations that follow Generally Accepted Accounting Principles (GAAP). ( Emphasis added)
I reached out to FASB to find out how they might feel about being made responsible for determining tax rules. What I found is that FASB refuses to comment on tax policy proposals.
The Warren Economists
The report from the Berkely economists that the Warren campaign sought out is not that meaty.  They used Compustat to come up with an estimate.  They pointed out a couple of ways the tax might be avoided, the most notable was corporate inversion, since the tax is only applied to US based companies.
Treasury regulations regarding corporate inversions have been significantly strengthened in 2016 and since then corporate inversions have come to a halt. The higher the effective U.S. corporate tax rate, however, the more pressure there will be on that front. The solution to the problem of tax competition from low-tax countries involves greater international tax coordination (in particular, reaching an international agreement on minimum effective corporate tax rates) and the adoption of defensive measures against tax havens and multinationals headquartered in countries refusing international coordination.
 I think that might border on the “assume a can opener” school of economics, but maybe that is just me. They come up with a ten-year conservative estimate of just over a trillion, but you might end up suspecting that they backed into the assumptions that would bring them to that number.  Well maybe you wouldn’t, but I’m a pretty cynical bastard.
I don’t think the critics are necessarily doing much better.
American Institute For Economic Research
I spoke with Edward Stringham of the American Institute for Economic Research.  Mr. Stringham has a PhD from George Mason University, but what really impressed me is that he has a bachelors from the College of The Holy Cross, so I know he has to have a lot on the ball.  We had a delightful conversation, although in substance it was a little frustrating.
Mr. Stringham thinks that Warren’s proposal is a very bad idea.  That was not, however, a reflection of the details of the proposal.  In his view, the proposal is bad because it represents an increase in corporate income tax, and corporate income tax is the worst tax that there is.
Other than bonding over our love for Holy Cross and appreciation of the works of Robert Heinlein, we did not get too much further. Mr. Stringham has a copy of The Moon Is A Harsh Mistress on his desk.  There is this whole libertarian thing about Heinlein, which you really don’t get from Starship Troopers.
Regardless, as I probed for what would be a good tax or at least a not so bad tax, he kept telling me about guys he knew who thought maybe this or tax might not be so bad, but he was unwilling to come out for anything.  His libertarianism is pretty hardcore.  He would just as soon social security were abolished.  Well, Mr. Stringham was born after I graduated from Holy Cross so it might look different to him in a couple of decades.
Tax Foundation
The dynamic analysis of the Tax Foundation has a similar negative bent, that I believe is inherent in their models evaluation of any tax increase.
According to the Tax Foundation General Equilibrium Model, this proposal would reduce economic output (GDP) by 1.9 percent in the long run. We also estimate that the capital stock would be 3.3 percent smaller and wages 1.5 percent lower, with about 454,000 fewer full-time equivalent jobs.
The Tax Foundation model does not account for the government spending that would be facilitated by the taxation.  In their model the government takes a trillion out of the economy and burns it in the backyard.
There is some analysis of the specific effect that makes the Real Corporate Profits Tax particularly bad in their view.
The extent to which the corporate income tax distorts investment decisions depends largely on how much of a given investment can be deducted against taxable income in present value. Under current law, companies can expense, or deduct immediately, short-life assets against their taxable income. Long-life assets qualify for accelerated depreciation. The result is that many investments are exempt or partially exempt from taxation. Under the surtax, however, companies would not have access to expensing. The result is that all investment would be fully subject to the surtax.
An Interesting Thought
There is a very interesting proposal kind of buried in the Real Corporate Profits Tax.  The notion is that at least with respect to RCPT, the definition of income would be significantly insulated from the political process. I did not see anything in the Warren material that indicated that it is FASB that should determine the measure of taxable income, but that is the effect.
I actually think that a case might be made for a system that worked like that.  It could shrink the Internal Revenue Code substantially.  It would preclude using the Tax Code as an instrument of social policy, which I think many of us think would be a good thing.
Something tells me that it is not really politically feasible, but I do find a beautiful irony in Elizabeth Warren proposing the privatization of tax legislation.
Other Reactions
Karl Smith had  Elizabeth Warren’s Corporate Tax Plan Sounds Reasonable. It Isn’t. in Bloomberg Opinion. The details of his discussion of GAAP versus tax are a little shaky.  He does make a very important observation.
The GAAP standards are conservative, so many companies emphasize alternative accounting measures that cast their performance in a more favorable light. Amazon.com Inc. chief executive Jeff Bezos, for example, has said that he doesn’t much care whether his company ever earns a profit as calculated by GAAP; his goal is to maximize another measure called free cash flow.
 If management is touting a different measure of profitability than GAAP income, is that what the real profits tax should be applied to?  Smith attributes GAAP rules to the SEC and as you noted I blamed FASB.  Both those answers are accurate but not precise.  When it comes to public companies the SEC has the authority, but it has designated FASB as the rule setter.
Brittany De Lea has  Elizabeth Warren’s tax on corporate profits would reduce GDP, wages and jobs: study on Fox, which is essentially riffing off the Tax Foundation with no reflection.
 Michelle Hanlon and Jeff Hoopes have  Warren’s corporate tax ‘solution’ is fundamentally flawed in the Hill.  It is really solid critique of the problems raised by the proposal.

The tax code does have flaws, and lobbyists do influence Congress to change the calculation of taxable income. However, the solution is not to do the same damage to financial accounting standards.

The best approach if Warren is worried about lobbying would be for Congress to take responsibility, not be overly influenced by lobbyists, and get the courage to write the tax code in the manner that is best for the country.

Hanlon and Hoopes are accounting professors.  Maybe the Warren campaign should have reached out to a couple of them when it came up with this scheme.