I've done several variations of binding trades, and haven't had any problems yet.

I've taken trades and added other issues to the back of them. When I was doing my Infinite Crisis set, I used trades for certain arcs/issues, because it was easier and cheaper to find. And in some cases, it meant splitting the trade apart after each issue contained within.

I took the first Ultimate X-Men trade, spliced in the original UXM #1 (because it was uncensored) and tossed UXM #1/2 in the back. Great results.

Currently at LBC is my Civil War project, which is nothing but trades that I split apart and rearranged in chronological order. The only single issue in the batch is Cap #25 Director's Cut.

The only "problem" I've encountered was using the GR/X-Men trade in my Midnight Sons book, because the paper was a heavier stock, and so the pages don't lay as flat at the rest, but that is a really minor concern.

I haven't done any project where I just slap two or more trades together yet, but I know I've seen examples by Mr. Banks where someone did a few volumes of Fables and/or Y using multiple trades in a HC.