the only thing i can say towards the whole iron man meeting with latveria prime minister and doom (and remember just because hes a kid doesnt mean he cant become a dictator, and once thats done im sure its not too hard to set up an entire government, plus he was wealthy and had means in the f4) is this.
In Ultimate Team Up tony says he wont sell the information over to anyone, and at the end of that issue even fury says that the US wants the tech. Now take this into consideration. (Just a theory) Stark is a multi billionare in the ultimates, not a soilder, he doesn't need the job with them hes doing it to do something with his life before he dies. In fact, if anyone is benefiting from having him on the team for his armor and celebrity status, its shield and fury. Just to point out, Nick Fury isnt the nicest guy in the world, we all just sorta grew to love him, think about that one for a second.
Now what my theory is in putting the UMTU with the continuity is this,
First consider Hank Pym might have hit something on the head. He mentioned The eccentric super heros and playboys are paving the way for super soilder grunts. Shield wants pyms Ultron design, and why has Banner REALLY been kept alive? Because he was one of the team? or for the sole purpose of getting more science out of him, i mean when the public came screaming for the hulks death, fury had no problem giving him up.
Also, Fury has access to examining the iron man tech before each mission to make sure the suits up to par (but lets say they are really examinging the suit) Maybe Stark catches wind of this and why he was REALLY invited to join the ultimates, (so the us gov. could steal the tech right out from under him) He quits, within a year or 2 UMTU occurs.
Like i said its just a theory, and its the best explanation i can offer to that team up issue, and the only thing i can really add to that is that in regulare marvel continuity i believe WAR MACHINE was a us government run program using the ironman technology
of course then u have to take each issue of UMTU as entirely seperate and not being continuous within itself which can be silly to some people