bedding vs caulking

Good for you, but I can't help notice that the OP is doing his now and we've had at least 4 or 5 others here in the past who've done the job. Some are more particular than others I guess. And you said you replaced a section. I'm assuming that you didn't run into 5200 or I might have heard you cursing all the way up here.

I just redid mine, Ocean Yachts, I cleaned out the hull/deck joint and sealed that with 5200 around the entire boat. Also sealed up the old screw holes from the old rail.
I used a TACO rubrail white rubber ''J'' type which runs just under the bottom edge of the hull up and over the joint to the flat part start of the deck. I ran a bead of 5200 centered behind the new white rubber part and screwed that on at the predrilled holes. Done. No caulk to be seen and the rubberrail makes a sung fit. Any caulk that came out is wiped up.

Then over that goes on the S/S rubrail which sets in a grove on the white rubber rail. You screw that in and through the with rubber rail centered , which is already caulked before, and run the screw through and into the hull/joint. No need to caulk the S/S rail as the white thick rubber seals up tight around the second set of screws. No caulk needed, nor should it be seen. No leaks.

it's actually not hard to remove 5200 from a flat stainless rub rail or most others. The rubrail is a nice flat surface and you can get a razor knife right behind it easily and run it down the backside of the rubrail and it cuts off pretty easily compared to 5200 in other areas.

What caulking is best to reseal joints like this on the deck?

I life Life Seal (NOT Life Caulk)

Ive found life caulk to be garbage. Life SEAL however is an excellent product that I use a lot for things like that and it does last.