This may sound dumb, but I'm wondering how to safely and properly drill holes for wires through the metal under the door. Hear me out,
What I'm going to do is mount LED lights to the under side of the door and then drill a hole on the underside nearest to the hinge, then run the wire behind the door panel, through the door-to-cabin grommet, then to the courtesy lights so that the LEDs will light up whenever the courtesy lights are on, ie, when the door opens and it will be a really cool automatic puddle light. Any tips regarding the hole drilling?

I'm thinking to protect from bare metal rusting, I want to drill the hole, paint the thickness of the hole to prevent rust, then put a shallow grommet in the hole to protect the wires and to not get in the way of actually closing the door. Sound good?
I'd like some other perspectives in case i'm overlooking something.

In your model year, the rubber boots that attach to the front door and body actually hide connectors inside them. This is also how all 2000+ rear doors are configured. Running wires through them will not be as easy as you hope. I'm not sure what the transition year was, but some of the newer Bonnevilles, the door harness connector runs through the body and is located inside the the foot well behind the trim panel. This makes running wires through that boot much easier. Regardless, I know your year will be a problem.

I helped harofreak00 add turn signal mirrors to his 2000 SSEi. We actually built wiring harnesses that plugged into the door jamb connectors using factory terminals in spare cavities. This would be, by far, your best solution.

Of course the inside of the doors is considered a 'wet cavity' (meaning it's intended to have water enter). I'd be very reluctant to drill holes in the door because of rust. You'll never be able to clean and seal the bare metal properly, at least with ease. If you wanted to mount lights, I'd stick to finding something flush mountable that you can attach to the door trim panel instead.

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Turn Signal Mirrors, Center Console Courtesy Lamp, Rear Outboard Heated Seats, PVD Chrome 18" Factory Rims, Upgraded
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