When I installed one of the short rail section on the bottom front of the 13" TRX hand guard, I had the same issues with contact between the rail backing plate and the gas block. I used a file on the back edge of the backing plate to angle it so that it could not contact the gas block.
I was able to angle it enough to avoid contact when the rail is flexed without reducing the thickness of the backing plate where the screw passes through it so it should be just as strong as it ever was.
I use a #10-32 sling stud to replace the flat head screw in our QD mount. You can get a sling stud from a local gunsmith, Brownells, or out of the JP VTAC kit if you had an extra like I did.
I tried the Harris HB5 bipod adapter stud, and IT WORKS without contacting the low-profile gas block. Also available here. I added a small washer that fits inside the Troy hole (between the two brackets) to center the stud and prevent fore/aft movement. The small bracket from the adapter fits nicely in between the leather slats from the Harris bipod such that the bipod will sit absolutely FLUSH to the Troy BattleRail TRX Extreme outer surface.