I just finished doing exactly what you are doing (removing/re-bedding caprails fwd of the genoa track).

I had to do a few repairs to the teak, particularly on the ends where water would wick underneath at the scarf joint and caused dry rot.

I completely removed all traces of the original dolfinite, sanded the surfaces with 80-100 grit, then cleaned everything with acetone. My experience with Boat-life and/or 3M anything has not been good so I rebedded the caprails using a generous amount of Sikaflex. And I mean generous.  I completely filled the 1" wide 'groove' next to the hull and probably smoothed on 1/4" layer of Sikaflex so as to essentially create a 'gasket' that would eliminate any/all voids period.  I wasted a lot, having to clean the squished out Sikaflex but I don't want to do this again.

But trust me, it's worth the effort the next time it rains and you have no leaks.  It's a really good feeling :)

Regarding your issue with silicone I think that only applies to paint/gelcoat. Once you apply silicone to paint/gelcoat any future paint repairs will then be problematic. In any case I believe if you sand the surface well and clean thoroughly with solvent you will be fine regarding whatever you use to rebed/recaulk the caprails.