So the orange lake pad and, moreso, the meguiars mf pad, knocked down that etching significantly. They are still there though. Not sure if I'll return to it with a more aggressive product than the ultimate compound -- or if it just needs more passes.
That's it for this year as I have another vehicle to prep for winter. Also, not sure how much clear I can or should remove without risking having lesser protection in place. Although my best guess is that water will continue to settle in those little voids -- making the problem worsen.
I want to thank everyone here and this site for giving me the confidence in proceeding this far. It took me over two days plus the experimenting on the hood. Here's a pic of the entire outcome. It hasn't looked this good in a long time. Not bad for a 130k daily driver that lives outside.