I figured I'd post a photo of sealed deck fill as a way to wrap up this thread. I did a lot of reading online and decided to give this suggestion a try. My Waste fill was looser than the fuel fill so I started with it. It would be nigh on impossible to reach the fill from the engine room without removing my A/C units.
I unscrewed the fill and took a small, round Dremel engraving bit and undercut it about a 1/4" deep and 1/4" back under the lip of the fill. I taped off a circle about an 1/8" larger than the fill lip with blue tape and used Teak Decking Systems black caulk to fill the space. I took a small plastic stirring stick and smoothed the caulk as best I could then left it for two days to cure.
Since the caulk was now firm, when I screwed the fill back down, it compressed the caulk a little bit and made a nice, tight seal.
It just rained 3/4" yesterday and no leaks! The photo shows the duct tape residue that I have not yet cleaned off. I also need to sand the caulk a bit to smooth the circle out.
Starting on my starboard fuel fill tomorrow.