Two points:
Costume Fitting: Anybody out there done any costume design? I have. And measurements for the costumes are made far in advance of production. Dude, you literally tailor that garment to the actor. Now, if say, two or three months from he or she has been going too one too many barbecues (possibly as in the Frakes case) or decided they were going to go on a diet because they felt they were gaining weight (possibly as in the Burton case) there is no way you're going to be able to adjust those costumes. You have a budget for them and when you use up the money (which includes tailoring costs) you're outta luck.
I think in Jonathan's case he gained weight after the measurements were taken. Afterall he was in his mid to late 40 and those of in that age group know that all of a sudden the weight starts creeping up on you and you have no idea what's going on.
Costume Integration: I'm sure they had a limited budget and were trying to cut corners anyway possible. The idea of integrating the DS9 costumes may have been Jonathan's way of helping bring the movie in on budget.