1. The use of the apartment while he was working in NYC and had his primary residence somewhere else (the Hamptons, I think) was legitimate. It would be no different than the Trump Organization covering the cost of a hotel room while he was traveling on company business.
2. When he sold his house in the Hamptons and lived in the apartment on a full-time basis, the apartment effectively became his primary residence and he was obligated to report the rental value of the free apartment as "constructive income" on his tax returns. If he failed to do this, he was guilty of tax evasion, tax fraud, or something similar.
3. The Trump Organization had no obligation to pay any taxes for this apartment. They may have been obligated to report the cost of it to the IRS on a 1099 form, but if they didn't know anything about the guy selling his home on Long Island they'd have no way of knowing that the apartment was his primary residence subject to reporting on the CFO's tax return.
If any Freeper CPAs are out there, I'd be curious to hear your input on this.
What a joke. You do not think this was a screw job?