I'd rather have a little bit of Allen head sticking out than the thought of ever putting a torx POS back on my Jeep. Mine sit flush.
I just replaced the windshield frame on my CJ about 2 weeks ago. I bought 8 of the counter sunk Allen head bolts. 5/16x1" is the correct size. I also replaced the bolts with stainless that hold the windshield hold down onto the frame. I used 3/8x1" countersunk to hold it to the dash. I put anti-seize on all the threads. I did put some black RTV between the hinges and the frame to keep water out.
When I put the new cowl seal on, it was very "inflated" to the point I had to use a ratchet strap from the top corners down to the seat frame to pull it back enough to get the hold down bolts in. Once it was down, everything fit perfectly.
Beat it to fit, paint it to match!
Wheel, Wrench, Repeat.