Seeing that precursors will just spawn out of nowhere - in orbit of the planet, with giant ships no less - after digging it up a bit, I think I'll turn the 'enhanced precursors' setting off.
I'll probably turn off for all of the special NPRs, as that looks extremely annoying.
Unless I decide I want some masochism for some reason...You put expensive equipment on the planet, only for it to be completely obliterated by an enemy appearing in orbit - with no downside for them, like jump shock.
If anything, this basically prompts me to ask for a similar tech for players and regular NPRs - fleet teleportation installation. This installation would allow the player/NPR to basically teleport things between teleport installations, limited by installation size. I think size 1 installation would allow 100-ton ship teleports.
But of course, the precursors are darn robots which can teleport, and the pathetic organics can't!

I mean, that would be my justification for why regular NPRs/Players wouldn't be able to use it.
Still, I guess some would like this grim aesthetic to things, but I think it would be better to give some kind of subtle early warning to player about upcoming awakening - like messages reporting odd tectonic activity or other strange seismic movement. Maybe xenoarcheologist teams getting attacked/buried by traps, or simply eroding structures. Leader of excavation team getting bad feelings about it or straight up killed.
I think whole planet getting glassed immediately is overkill, it needs to happen gradually, with subtle things happening at first, and then as you complete digging it gets up.
I do wonder how would've campaign went if necrons woke up immediately on Mars the moment you started digging it?
EDIT: I guess recovering goodies (installations and fuel) from them is good as a compensation, so there's that at least.