The LiPo rubber or foam pad isn’t quite thick enough or I need more protection.
  After seeing the dents I started sandwiching a sheet of plastic between the M3 screws and LiPo and it’s working but is there materials used that are glued to LiPo.
  
  Here is a picture of what I’m talking about and instead of sandwiching something in each time I need a permanent fix.

I use 3M duallock on the frame and lipo to prevent lipo ejection. But it is also thick enough that I don't get screw head dents.

Normally I would argue that you need to join "Team Ummagrip", but on this rare occasion I will side with "Team 3M Dual Lock" This is because you can attach a piece to both the quad and the LiPo, so you will also be protecting the LiPo with the piece you attach to that

I might have some around the house.
I like that much better than the foam and I can see the M3 sharp places eating away and causing a LiPo disaster

one vote for joining team ummagrip :-)

Where is team duallock? Krohsis?

There’s some silicone cell phone holders that might work too but likely heavier.
I like the dual lock Velcro and have used it on planes.Sometimes need a broken prop to pry off the LiPo but better than a short or flying LiPo.

Countersink the screws and use flatheads. ?

Just my take on it...

I use Soft Touch Self-Stick Non-Slip pads  which are thicker than the height of the bolt heads. It is also "Stick on". The "Soft Touch" grip pads tend to be a little thicker than the Ummagrip {which I have tried, but rarely use; I like the other stuff better}.

Take a close look at this picture of Katana-LR5x. I notched the pad so I could get to the bolt. 

I have also tried the "Dual Lock" {Velcro} stuff, too, but I don't really like it, partially because I don't want to stick it on every battery that I have. I use a variety of batteries and battery combinations, so the "Dual Lock" just doesn't work for me.  I tried it, but didn't like it.