The 2.5" collector will not make a difference when it starts to crack. As far as the tubes with Banks and Borla, they follow stock because they have to bolt up to the stock down-pipe (Cherokee and Wrangler). Borla comes with its own stainless down-pipe, but it is only 2.25". As for Borla and the 2.5" collector, it narrows down to 2.25" so the collector is a moot point. Something like a bottle neck. I ordered a pair of Banks headers as my replacement for the stroker I am building. But after looking at the welds (MIG) on the headers, I realized they were sh*t too. I sold them "un-used" to a guy with a Wrangler. JBA, Clifford, and Doug Thorley seems to have it done right.
Another thing to eliminate potential cracking caused by vibration resonance from the down-pipe would be to put in a stainless "flex joint" somewhere between the collector and the catalytic converter. You can get these from people like JEGS. And yes, with Clifford or Doug Thorley headers you will have to "build" your own down-pipe, or exhaust, before the cat. But this is easily done with people like Jegs or Summit Racing.
I thought the same as you and bought Borla.
But that was before I found this site.
Good luck.
KJ