I'm trying to get rid of my pedestal spoiler asap and I just remembered that
the pedestal spoiler, installed, requires you to drill holes into the trunk.

Taking it to a body shop to be filled in with... bondo? Would be my first choice,
but I don't feel like spending any more money.

I was wondering if you could buy like, silicone sealant from Home Depot and
just fill it in. And after that, buy touch up paint from the dealer and just paint
over it.

Take into consideration that I'm going to purchase the V-Style spoiler so the
holes would pretty much be covered by it. I just need it to be water-proof.

Anyone?

If the holes are not gonna be visable you could do that, so long as their not letting water in no worries. ...dunno if the touch up paint will stick to the silicone tho. Since your BSP you could use Ultra Black RTV sealant its about the same color as BSP. I'd just takt the trunk liner out, put some tape on the top of the holes and smooth some UB RTV sealant on the back side. Put the liner back and peal the tape off the outside of the car once its dry and there you have it smooth waterproof nearly invisable patches, then cover it up with the new V style spoiler.

...you could also do the same process with bondo and have em spray it when you get the new spoiler painted.