From my perspective and I have scene this done quite a bit. Most opening have a dbl stud on each side if the opening, by replacing one pc of the 2x(1 1/2" thick) material on one side and or possibly both sides with what is called 5/4 material(1 1/16-1 1/8 depending) you will gain at least a 1/4" just from one side. And i cannot see how it would effect the structure at all and i have never been told any inspector had a problem with it.

Talk to the Integrity rep. I think you are going to be okay in that they allow a full inch in width and a half inch in height difference between rough opening and net window size. I would give your contractor the net window sizes that Integrity gives you and let him work with those.

Thanks Eastbay10, was going to post a follow up confirming what you said.

Now I have another dilemma, will post a separate thread.

Thanks

If things are tight you should be using Marvin's "frame dimensions" rather than rough opening dimensions.