As already mentioned above, a thin plastic auto trim tool can be used to get under the molding (or even a credit card), slide it over to a clip and pry upward. Or, if you remove the interior cargo area panels, IIRC you can push up on the clips while squeezing/bending the tiny tabs that poke through the holes.
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Been discussed a lot but FWIW, IME/IMO there are better sealants (than silicone) to use if you need to seal a leak, if you use silicone it will be much more difficult in the future to remove the molding. Also there's not much space under the molding once it's installed, a little too much sealant/rubber and it will squeeze out from under the molding and make a mess.
FWIW I've used put a
very small pea sized button of
butyl rubber tape/rope (3M window weld) over each clip hole then reinstall the molding. Or if you have a leak and you don't want to remove the molding you can put a small button of butyl rubber (working inside the quarter panel cavity) over the bottom of the clip and the hole. I've also used 3M strip caulk (small pea sized button) and it worked but IME it makes more of a mess if it squeezes out from under the molding. (easily cleaned up with a paint safe mild solvent or rubbing alcohol).
As you mentioned the new molding comes with very thin gaskets around each clip that are meant to seal the hole so they should be good enough, at least for ?? years. But then you could use a small button of a non-hardening product and forget about it for the next 30 years, main thing to keep in mind is that it doesn't take very much to seal around the clips and any excess will squeeze out.