which is the better option?

custom catback. will be mating to the stock dp (for now)

2.5" from dp back, 2.25" y pipe to mufflers

or

3" from dp back, 2.5" y pipe to mufflers

3" from DP back to y, with resonator. Split to 2-2.25.

Pi * 3 = ~9.42 square inches.

(Pi * 2.25) * 2 = ~14.14 square inches.

It still is an increase in cross section for two 2.25 pipes over a single 3" pipe, so it shouldn't be a bottleneck if the split is fabricated well.

The 3" main pipe will mate well to an aftermarket down-pipe in the future, unless you KNOW you won't be doing that upgrade, then 2.5 will probably work. The larger pipe will also allow expansion, which will drop back pressure, and exhaust velocity, which will in turn help it be quiet, while not corking the exhaust system up. A resonator in that pipe will do so even more.

2.25 is probably a more common diameter for mufflers and tips, unless you have some specific 2.5 inch mufflers picked out. Probably easier to go right to 2.25", rather than having to reduce it after the split.

a lot depends on what mufflers you want to use, though.