rebedding deck hardware

[osteoderm]

I too have been long-seduced by 5200, but am starting to move away from it for many bedding situations since I've found better products. I find it far better to regard 5200 as a glue rather than as a bedding. It's the best for pretty much permanent installs; through-hulls, extruded toe-rails, hull-to-deck joints etc.
With fittings subject to cyclical stresses from differing directions, some pad-eyes and definitely stanchion bases, the mechanical fastenings must be closely-fitted through properly-sized holes, any deck-core must be replaced by solid material in way of the fasteners, and substantial backing plates installed. I think that 5200 adheres strongly enough that it makes up for the wiggle in otherwise less-than-perfect installations.
Benz, I'm sure you've encountered this: a leaky stanchion base, poorly fit to the deck (maybe right over old non-skid?), fasteners through sloppy holes, stacks of fender washers below, and whatever old bedding all crumbled, dry, and poorly/inadequately applied. After cleaning off the old bedding surfaces and re-bedding with 5200 (plenty of squeeze-out, no air pockets), well yes, the leak is gone... but the essential underlying problems are not. I'm sure we can agree that no goop is a cure for inadequately-installed hardware.
If you've really gooped it down well, any removal will be a pain, and if the cleaning and application are at all wrong, the stresses and movement will eventually open a seam somewhere; 5200 is really only marginally flexible enough, especially once exposure has further hardened it, and relies entirely on adhesion to resist shearing forces.
Traditional "soft" beddings, either oil-based from a can, or basic 3M 101 in a tube, require a solid mechanical connection between pieces; they do nothing to hold things together or otherwise firm up a less-than-perfect situation. However, when things begin to creep and shift they work into seams, and there's no hard glue-line to break under shearing loads.
Then there's those "whoa-geez" situations when you just need to get something back together quick'n'dirty without a lot of prep hassles. Many sailors keep a tube or two of 5200 around just for that. In my locker, that's been replaced by a couple tubes of 3M UV4000 Fast Cure, but whatever works.

To address the original question: different applications, different goops; there is no single "absolute best compound". Ultimately, it's better to strive for perfect mechanical connections rather than rely on goop.