I recently re-bedded my through bolted ports with butyl, worked well. We have had a few big fall rainstorms with no leaks yet. Most of the points have been made, but...
I agree with "cutting" the butyl ooze with a putty knife prior to the stab and pull step. Otherwise there is a tendancy to pull some butyl out of the seem.
Get all of the old stuff off, it will be hard if it is silicone. I used Mainsails method of a sharp chisel used very carfully at a low angle to get it off the gelcoat followed by wet sanding and a final solvent wipe.
Use lots of butyl, it is cheap. It will slowly ooze into the nook and gaps if you do it on a hot day and go slow. It is much easyer to clean up than most caulk.
The stuff sold through his compass marine site really is better than what was available at my local RV dealer. It is the proper thickness for port work and although stickyer, is easyer to handle because of its size and packaging. I found that the corners of the ports tended to get starved of butyl, and a double layer helped, the strait sections did not need as much, your milage may vary.