I've heard good and bad about several of the ways we've discussed

Grease
Good - It traps the metal flakes as the drill bit cuts
Bad - The flutes of the bit are made to channel the shaving away. Could become clogged and drop greasy sticky shavings into the turbo

Drilling while idling
Good - Blows the shavings out and nothing falls in
Bad - Ever broken a drill bit. What happens if you do break a bit off while the engine is running. So long turbo.

Removing the manifold
Good - Safest way to ensure no shavings get into the turbo
Bad - Time consuming. Could have leaks. Could break or strip a bolt or nut.

Again, it comes down to a comfort factor. I'm more than willing to spend a few extra minutes to do something I know won't damage things. I can fix a stripped stud, nut or leak a whole lot easier than I can fix a ghosted turbo. Heck, a new, stock exahust manifold only runs $115. How much is a new turbo? $1500 - 2000.

I guess if I wind up going that route, I'm just gonna drop the cash on an ATS manifold anyways.

 

Once again it is all in how you feel the safest route will be for doing this. I can tell you this, 25K later I have no problems with my turbo just drilling straight into it. one key part is to make sure it is on a cold engine. that way if you do have some small left over bits it wont dammage the turbo since it is notspinning as fast as if it were hot.

If you dont feel safe drilling it in place, then pull it off. . .however if you do decide to drill it in place, be sure to clean the bit often to keep as much gunk from falling into the exhaust manifold. this is especialy true when you tap the threads.