So I'm getting a 3" exhaust put on the car and the guy is also putting in a new flex pipe that is leaking/crushed on my BEGI DP. Are there much gains to be had to have him bump that section up to 3".
Looks like the BEGI is 2.75" stock and the area I would supersize is maybe 12" of length. Also not having looked down there in a while are there clearance issues at that area of the car with the 6spd tranny and a 3"

Thanks

 

Only clearance issues would be in the area where the transmission meeds the engine.

Since the section you're talking about is not in that area you will be fine.

if he's going in there and cutting/welding why not get it redone in 3"? it only makes sense.
My current downpipe is exactly like that actually. Check my build thread for pictures.