I opened up the ID of the ball flanges on my diy headers to about 2-1/4" because I had 2-1/2" OD tubing (2-3/8" ID) from the collector to the flange and the ball ID was only about 2-1/8" originally. However, TMH collectors neck down to 2-1/4" OD (2-1/8" ID), so the flanges themselves aren't any more of a restriction than the tubing leading to them.
I will say cutting off the flanges shouldn't be bad at all, I removed my TMH collectors with a hacksaw and everything came out clean. It shouldn't be any harder to re-weld the collectors than butt welding tubing would be. I'm having a coworker TIG that for me once I get the holes filled.
Long story short, converting TMH to a different flange style would be pretty reasonable, but making them bigger wouldn't be as straightforward. You'd probably have to splice in a different collector that doesn't neck down for 2-1/4" tubing. That sounds complicated, but wouldn't be impossible by any means. Just cut the original collector off like I did, use it as a template to mark a new one, cut, re-weld. Good excuse to go with larger diameter downs and v bands all at once.
At some point though, the primaries will become the restriction. I'm not sure, but it would seem to me that 2-1/4" collectors might already be appropriately sized for TMH 1-1/2" primaries. If you upgrade to 2-1/2" or 3" downs, you might not see gains without also going up to 1-5/8" or larger primaries. From what I've read, you don't want the downstream exhaust to be oversized compared to the beginning as the increase in volume will lead to slower exhaust flow which can reduce efficiency of the system overall. That may not be as true for a boosted application though, definitely worth further research.
