As usual, I find myself agreeing with your points.
The biggest issue for me is that the huge cases are really not required for the WR boasts. I have very small, slim dive watches that are 200m ISO rated. I have seen G-shocks with pressed metal backs with 4 screws that failed by deformation at 3000+m.
So the huge cases are, to me, not required for performance or engineering reasons, rather they're for 'demonstrating' the greatness of your unusable depth claims.
[I also finally worked out the usefulness of the chronograph complication that you were explaining, good point concerning the safety stop extension. The countdown feature on my G-shock is useful for this....air permitting. No problem pressing buttons at 5m...]
The alarm function is interesting. I sometimes use the dive-time alarm on my aqualand, which also has a normal alarm for waking-up...The issue you raised with the resolution (12min) of the markers on the JLC is a good one, not to mention the general resolution of a 12hr dial as dive timer is not ideal, as a general warning (say, set to the NDL limit) it might have some use.