Here was my experience which you may find helpful: 240 windshield trim removal/installation 200 1989

Use a hair dryer to force warm air in there to get rid of any moisture, and don't cualk it right after a rain. Caulk it after a nice long warm day in the sun. If you use masking tape to mask off all but just the skinny little crack where you want the caulk to go, you can be as forceful as you want about pressing it into the crack without have to worry about making a mess. When you are done pressing it into the crack, just smooth it out with your finger and then remove the masking tape. The resulting job will either be invisible, or will look neat enough to pass for stock, if you've masked carefully enough.

If you are caulking in between the seal and the frame, use black RTV silicone. If you are caulking between the seal and the windshield, use clear RTV silicone.

Ever hear a dealer say "they all do that"?

The trim doesn't seal the windshield, but you're right it would trap more dirt which holds more moisture. The problem is the clips are brittle and are bedded in the real windshield seal, making them a bear to replace even with the soft butyl rubber gasket, but impossible if the window was put in with polyurethane. The clip kit is available from dealers and others - not expensive, I think around $20. But you might find a windshield shop will be experienced with fixing the trim without pulling the glass, and may find it isn't outrageous.

Slathering it with silicone RTV never works for long.