I had the same problem. I got an MRT hpipe 2.5" and actually ordered the wrong flows 2.25" to go with them. I didn't realize this until after it was all put on (flows welded in) and there was a small gap between the piece which connected the hpipe to the catback. I eneded up taking it back in and they cut a piece of the flowmaster pipe off (like 6" off right before the muffler itself) and welded on a 2.5" piece of pipe of the same length back on to the muffler which inturn made a nice even fit to the hpipe.
Bottom line, of course you would want the 2.5" flows to accomodate your 2.5" midpipe, but it's not a show stopper. Whoever puts it on can do the same and you can keep your exiting flowmasters. You won't see any noticable loss by doing this, in fact, if you're replacing the stock H, you will see nice gains and sounds, and not worry about the mismatch between the midpipe and catback.
Hope this helps
Later