What would be wrong with using headless screws, screwed into the action, to keep everything aligned, and allowing everything to settle into the bedding on its own? Wouldn't that guarantee that the bedding job would be 100% stress free?
Also when you say you run a drill bit through the pillars, are you removing any material, or you just making sure they are clean?
You need something more than gravity involved in getting the action to "settle". The bedding I use is thick and if I relied purely on gravity, it would begin to cure faster than that action would settle.
I draw the screws up snug but not tight (and especially not farmer tight) and allow everything to begin curing for a couple hours, then I use masking or electrical tape to keep everything in place and back the screws out.
Works for me...as for the drill bit, not really sure what they're talking about.
When it's all said and done and the action is popped out, I do run a bit through the screw holes to get rid of any compound that seeped, squished or otherwise ended up in there.
I'm not a pro at this, but like I said, it's worked will for me each time.
Good luck,
Rob