Mounted a gemtech flash hider onto my steyr aug barrel.... and theres a LOT of barrel threading available since the flash hider doesn't screw all the way down. Is it safe to put the check nut on below the flash hider to cover up the visible threads? Or could check nut with gemtech flash hider cause a misalignment and baffle strike?

I can't say whether using the check nut could cause an issue. But fwiw, I don't think it's necessary.

I'm using AAC mounts on 2 of my barrels, a 16 and 20 in. I forget which one without looking, but on one barrel using one isn't really possible in my opinion. And one leaves a bit of threading exposed. I just slathered on some Rocksett and cranked them down. Nice, solid and no issues.

Thanks, the can seems to run fine without the check nut..but man its ugly with a good quarter inch of threads visible. I just want to make sure putting the check nut on to cover that up doesnt tilt anything out of alignment.
Good to know on the aac part though. thanks.

In my experience, AAC on the 20 leaves a little bit exposed, AAC on the 16 looks great.

Yes, I believe that's how it is on mine. Looks a bit funky on the 20. But I don't even notice anymore.

The real answer needs to come from Gemtech. Some suppressors or adapter mounts are designed to index on the barrel muzzle, while others need to index against the shoulder (where the barrel widens to it's original thickness behind the threads).

Here is what GemTech's online manual states:
Elite Iron specifies to index theirs directly against the shoulder, and to not even use any kind of crush/peel washer or spacer of any kind. I had to get an extended mount from them to fit on my Tavor that uses a jam nut on the factory compensator. Reading #3, I would say they might prefer that you use some form of spacer. I still go back to my original statement, that you need to give GemTech a shout. In the end, they will be the ones you will have to deal with if something does go wrong. Therefor it is best to let them decide/advise on how to properly mount it.