The bolts that come with the unit are what I would describe as pan head, mushroom head, etc. depending where you look. So they have a low profile and are rounded, as opposed to something like a capped head which is very prominent (think about the bolts used in 8020 profiles, that's capped head). So with these screws, even if you rest your head against them, they aren't really prominent and you barely feel them. That said, I barely rest my head completely on the head rest while in the rig, and even when I do between races, I can't feel it. Not sure if my head is just simply missing the bolt or it's such a low profile that I'm resting on it and I cannot tell.
For the drilling, you'll need to be careful. I had to drill through the fabric on my Sparco Rev, and while there is barely any padding up that high, the drill bit still catches the fabric and can pull as you drill. You might want to do some reading on drilling through material that is wrapped in fabric / padded just for your own peace of mind before trial and error-ing on your own seat.
The bolts you will more than likely need to source yourself, as you will need longer ones. Just take the ones that come with the unit to the hardware store and get the same spec but in a longer length. Someone there should be able to help you. Get long enough to reach but not too long that they won't be able to be torqued down and hit a bump stop inside. You may need to cut them depending how you go but you should be able to find the right length. You're correct, the unit rests against the back of the seat and the bolts go from the inside of the seat (where your head sits) through the seat and into the unit on the back. You may need a second person to help you hold the unit while you locate the threaded hole with the bolt. It's tricky.
