^^^ I dont know how much your statement is true. Yes any change in size will cause disturbances but the exhaust is a tricky model to use Fluid dynamics on. First you are pushing the air through a valve in the head which will cause "turbulence" at the very start. Then you have the turbulence from the junctions in the header, Then the Flex section of pipe is ribbed so you have all sorts of things with that. And to mentioned all of this there are "burs" from welds and unless Mandrel bent you have size variations in all the bends from the head to the flex.
It will be best to stick with what ever size you choose for as long as you can.
Will you see any performance change, by changing a 3-4 foot section from 2" to 2.5? Most likely not, you may get a different sound because you have changed the resonance of the cavity.
Exhaust gas will move slower in a larger area, that's why most people only go with 2.5" if NA and 3" if FI. IIRC 2" single exhaust can support up to 200 HP with out restriction, 2.5" can do up to 300-350 and over that 3"... meaning if your at 200HP, you will not see any noticeable change if you upgrade from 2" to 2.5".
If it was my Foci, I would cal shops and see what shops could do with your muffler, and if they can make the opening 2.5". If they can then its up to you how you want them to proceed, either have the shop do all the bends out of their stock, or get a tube kit from a place like TruBendz, have been a lot of discussion as of late with them...