Usually Honda sticks an EGR on the automatic transmission version of an engine.

Evaporative emissions refer to fumes released by fuel stored in the fuel system; they have nothing to do with the exhaust.

As for the exhaust setup itself, if it can be made into a full 2.5" system by replacing a couple of sections then I guess that is a workable solution.

I'd wager a guess that as long as the cat is functioning properly and there are no leaks, you should be fine.