Are you saying that the IRS will literally officially modify your recorded / reported income and expenses to be different from what you reported, at their discretion, even if based on what they think are plausible reasons?
That still seems like heavy handed overreach to me. Should they not instead contact you for clarifications about the ambiguity?
This is required to make some people honest who would otherwise report $1 income every time. They have to work a bit harder to optimize the tax.
Well, they'll express their disagreement in the form of a letter and then calculate what they think you should pay and how far behind you are on the usual withholdings as a result, along with penalties.