Mr. R. Oh dear. You've hit upon one of MY major
dislikes-silicone caulk/adhesive. IF you insist on using this devil's glue, don't expect to ever
be able to paint or varnish anywhere in proximity to it.
I would strongly advise to use almost anything else. I have had good results from LEXEL. LexelŽ by Sashco - Silicone Caulk Alternative
Mr. OC's suggesting of masking is good.