Woodrich Timber Oil stain over caulking?

I have a new deck in Florida, pressure treated pine, finished one month ago, in full sun. I plan to prep and stain it a month from now. The builder caulked a number of joints where the deck goes up against walls, screw holes, etc with what looks like white silicone caulk. Will the Timber Oil "warm honey gold" (I have the stain already) cover the white spots, or will I have to sand that off? If I sand it, will the sanded areas appear different after staining?