Your tech's seen the guitar and I haven't, so I can't really challenge his opinion about the wood being too soft, but I doubt there's any danger of the guitar falling to pieces.
Stripped screw holes could be due to soft wood - and mahogany is a relatively soft wood. They could also be due to the pilot holes being drilled slightly too big. I remember when I dismantled my SE EG a few years ago I found they'd used very small, thin screws to hold the scratchplate and jack plate - I just replaced them with slightly bigger, longer Fender-style screws. Stripped screw holes can also sometimes be fixed by putting a drop of superglue into the hole to harden the thread (let it dry before putting the screw back in!).
Having said all that, you still shouldn't have these problems with a new guitar. It's definitely worth contacting PRS.