dealt with this exact same issue. First off, the spoiler seals via grommets, so using self tapping screws will just ensure your trunk will rust in three years. For the holes that stripped out, most hardware stores sell this fastener
Amazon.com: Jili Online 6 Pieces M5 Metric Rubber Grommet Rubber Well Nuts Blind Fastener Windscreen Wellnuts Kayak Accessories: Automotive All you have to do is run a screw with some gm sealant through it and the holes in your trunk are sealed. These aren't probably the right size, the link is just so you know what I'm talking about. For the ones that don't spin, just use a set of rubber washers like this
Isolate It: Sorbothane Vibration Isolation Washer 30 Duro (.13" ID - 0.5" OD - .13" Deep) - 12 Pack: Amazon.com: Industrial & Scientific to seal. Just make sure you clean the surfaces well before you install these (again, link just for an idea, not size you'll need, just go to the hardware store and size them with your old bolts).
From many, many tries, there isn't any great sealant that'll actually seal your spoiler directly to the trunk without having to sand and repaint, but then it becomes a "pool" up there (trust me). Better thing to do is space it up with the aforementioned fasteners to seal the holes. This also spaces the spoiler up a tiny bit. Not enough to be visibly different, but it'll drain better so water won't pool.
If you're still having a trunk leak, try putting some rubber washers around your taillight holes as it commonly leaks here. Another point is the body sealer by the rear taillights sometimes cracks (mine did). Just have a friend pour water on the trunk while you're sitting in it with a flashlight. You'll be able to see the leak with the carpet pulled back.