I switched last year from a D500 to an A1, and whilst there can be no doubt the A1 is better, I think that for the average amateur (i.e. me) or even advanced amateurs, there really isn't a great need to upgrade the D500 - its just that I had an A1 for topside (where it is far far superior) so I decided to stick with one overall system. I certainly wouldn't cry too much if I had to return to the D500 underwater.
For AF, I'm a big fan of continuous AF for most subjects other than when I attached the SMC-1 at which time I felt the D500 struggled (or maybe it was me struggling!) so then I would lock focus with BBF and rock the camera to get the picture sharp,
I see people using AF-S and if it works for them, then great. Maybe they are better divers than me and can hold rock still in surge and current (like I had to watch my annoyingly talented dive guide do recently in Tulamben) but I always prefer continuous focus as even with relatively still creatures there is always a certain amount of movement, either the critter, the photographer, or due to water movements.
I was happy enough with single point for smaller creatures and maybe I used expanded AF a couple of times with the sharks at Tiger Beach, but the best thing about Nikon AF compared to Canon and even Sony is its simplicity and that it just works for the vast majority of underwater subjects. I certainly had a great hit rate for both reef fish, gobies, bennies etc, along with close up sharks using this technique without getting into the 3D focussing. Maybe if I dived more often I would experiment more but I don't get that many opportunities so I kept it simple and it worked for me
I've never even considered spot metering for underwater - its not needed on the reef for regular reef fish and macro, and for wider stuff with water backgrounds I just took a reading to get the background how I wanted it then filled in the foreground subject with manual flash. Once you get an idea of power settings you realise that you're often working at similar distances so not too much fiddling about was needed
I also regularly use higher ISOs than most underwater photographers as I'm used to using high ISOs topside in crap British weather and am used to processing the shots accordingly, so don't be scared of pushing the ISO to get the settings you need. With a D500 I wouldn't even break sweat until ISO 1600 and hight is easily done with a little care in post.
Mike