You sure ask a lot of questions.

In your opinion should I even ask about the comingling or transfer of funds?

I don't consider having a joint bank account (if there was one) as the "transfer" of funds that the statute mentions.  I wouldn't ask.  IRS is not in the marriage counseling business, all they care about is that someone pays tax on all the income without gaming the system to distort the result.  Since splitting the income usually results in the lowest tax, any deviation from that is going to increase the tax collected, and Billy Long will be as happy as a Missouri hog, not that I am implying in any way that he resembles one.    

Also, no matter what, the spouse if married HAS to report the spouse's name and TP ID, correct?

I don't know of any statute that requires that.  Do you?  IRS may refuse to accept returns filed electronically without both SSN's but that's just their way of finding out how high you will jump.  

 do they have to follow the itemized versus standard deduction rules and do it the same way?

Why not?  But remember, Section 66 only relates to earned income.  It doesn't say anything about splitting deductions.  Might be difficult to figure out who gets to claim them, or whether they have to be split.