Yes I agree..although the first movie had a scene with the then-current president, he didn't have a big role and it was just a 'funny' moment..this time it's a bit weird the 'president' is giving out orders that have clearly been written with a more 'general' character in mind, only to have Bay include him in the movie by name, thus making him that character.  

Personally I think it's only a minor incoherence problem, there are far worse, but yeah, it is there.

 

Perhaps the debate to make the movie timeless or to place a date on it was still going on during the filming. Some films don't like to put a date on their films by using a generic president while other films don't mind putting a date on a film by using a historical president.

But I agree it's a very minor incoherence problem that doesn't really have any real impact on the overall movie.

 

My very basic understanding of the rules is that if:

The studio is caught with a scab writer, in this case Bay, they could be put on the unfair list. Essentially, Wga writers would no longer for for that studio.

The scab is prevented from ever joining the guild at a later date.

If a wga member is caught working during the strike:
Discipline may include, but is not limited to, any or all of the following:
expulsion or suspension from Guild membership, imposition of monetary fines, or censure.