Take a philips head and file the tip down. You now have a Posi-drive, which should prevent stripping the screws.
I can't see any possible way to mess up our skis from unscrewing bindings unless you're like Homer Simpson and start a fire making cereal.
Rescrewing into preexisting holes DOES compromise the integrity of the mount. When skis are mounted, the holes are drilled with a smaller diameter than the screw so that there is a great amount of inward force being exerted on the screw, thereby holding the binding in better. When you unmount, these holes "relax," and if you put bindings back in, the wood does not exert the same pressure and mount will not be as solid.
Also, wood glue has no direct effect on the durability of a mount. All it does is seal the holes from water (assuming you glued them correctly without air bubbles), which can potentially seep in and rot the core, making binding rip-outs easier.