Overall, the gun's balance will probably suffer.
What feature are you getting for the trade off? Because you can have a flash hider as long as it is pinned or welded on; and that job is a lot cheaper and easier than making a thumbhole stock, or buying one.
I have ARUL and a PRS stocks on my CT AWB compliant guns. If you get a suppressor, you'll need a pinned or welded q/d muzzle device...otherwise, just get a barrel that doesnt have threads and leave off the F/H. Muzzle brakes tend to make atrocious noise for the guys shooting near you anyways.
M1S an BCM will pin and/or weld a muzzle device for you if you order an upper from them, just call and ask for it...and bayonet lugs don't add a lot of utility anyways, so get a low-pro block or one with a 1913 rail up there.
I've also found that you can generally buy the parts for your upper individually for less loot than an assembled upper, and it's easy to assemble them. (Just don't call it a "build"; unless you fabricated the pieces yourself! / pet peeve) That way you get the features you want without having to compromise between the pre-assembled offerings.