Not sure exactly where you plan to mount the heater -- presumably on the forward port bulkhead in the main salon -- but depending on where the chimney exits to the deck, you may have to address the issue of deck camber.
We used a "Large Canted Teak Winch Pad" which helped to compensate for the deck camber. Otherwise, the chimney cap and shield hardware would be mounting to the deck at an angle very askew from the vertically plumb chimney.
There really is little concern about exposing the teak to the heat from the chimney. While nominally 3", I seem to recall the chimney is actually about 2 5/8" or so in diameter. This leaves a nice gap all around when you cut a 3" hole in the deck and the winch pad.
Also, the chimney is double walled, with air from exterior coming down the outer flue. This insulates and cools the inner exhaust flue (especially up near the top, where both the exhaust and intake air are cooler), so it does not get nearly as hot as a single-walled chimney.
As for capping it off in bad weather. I think, with the standard spray guard, that you will be in good shape for all but the nastiest conditions. That said, I too would devise a fallback for off-shore.
I think your approaches above will work pretty well. Seeing as I'm congenitally lazy, I would favor an approach that would not require any disassembly. Instead, I would want a solution that merely allowed me to cover up the cap and guard without taking them off.
I think what I'd do, is tap a small threaded bolt hole into the flat metal bands at the tip top of the cap guard. I would then permanently secure (epoxy?) a large nut on the underside of that hole. Then I'd hunt around and find a stainless steel kitchen bowl that was sized such that it could be placed over the entire cap assembly like a dome. I'd drill a similar size hole in the center of the bottom of that bowl. Then I'd get a bolt and secure the bowl to the cap guard, through the pre-drilled holes.
I would probably gasket it a bit too. A small rubber gasket at the bowl bolt. Then, probably a donut shaped gasket that would fit over/around the cap and guard assembly, lay on deck (or better yet the winch pad --that camber issue), against which the stainless bowl would snug.
Anyway, all this in theory -- I haven't attempted it. Hopefully that made some sense and you could follow what I was getting at.
I still don't have a good photo of it, but you can see our cap, with shield, mounted to the winch pad in this photo:
You can see that the canted winch pad did not alleviate all the camber, but it made it do-able.