I wouldn't count on 5200 to keep core dry. You might get lucky, but why have to? The other thing is if you have to remove them for any reason (damage, upgrade), 5200 can be a bit of a bear that way.
What I do for most* core penetrations is overdrill (by a goodly amount if below the waterline because I want a thick annulus that won't crack at all), treat with neat epoxy, then fill with thickened epoxy (colloidal silica, WEST structural filler, etc.). When that cures I do my hardware install (which may be through bolted, tapped, or whatever depending on the application). The hardware then gets bedding compound (again choice depending on job), which does not have to be super-ultra adhesive (which is what 5200 is). That way I have the core protected, the hardware fastened, and bedding compound between the two that can be removed or renewed as desired with no huge fanfare.
I drilled and tapped the epoxy plugs for my trim tabs, then fastened with bronze cap screws (non pointy); but you could also use "pointy" screws if you wanted to. Main thing is to protect the core (for which I don't like to use an adhesive caulk on the surface).
Doing things this way is not particularly difficult, but it IS a bit more time consuming and "fiddly" than slapping it on with 5200. There is also the fact that many instructions basically tell you to do it wrong (even Bennett, whose trim tabs and overall customer service I really like, tell you to just dip the screws in epoxy and run them in). So you are sometimes stuck trying to justify your way (if you are asking someone else to do it). Aggravating. I've just ended up doing things myself because I care the most about my boat and then I can do it how I like (not that one should have to of course).
Here is another link to a good photo tutorial. Even if one is not doing one's own work, it's good to see it I think. Basically many of us are describing the same concept, but just with little variations in tools used and methods. It's actually kind of fun to build up your bag of tricks for doing this work (or maybe I'm just warped

)
Sealing core:
http://www.pbase.com/mainecruising/sealing_the_deck
Bedding (specifically using butyl, but you can extrapolate to other choices):
http://www.pbase.com/mainecruising/rebedding_hardware
Sunbeam
*Sometimes I would close out the core by removing it, but not in this situation.