As I stated in the How-To, I was going to use the silicone lube, just as you figured out, to lubricate the re-installation of the weatherstripping. In the end, I did not need to do that, since doing a test fitting, it went on with no trouble.
Yes, mine also had that white/cream colored caulk. I did not wipe it off the weatherstripping. I left it on and re-installed the weatherstripping. I assume it has some form of extra water sealing function.
Mine has been bone dry (inside the car) since I performed the repair.
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