Nice upgrade man, that Key500.1 should definitely give that DS18 the power it needs - curious how you're finding the tuning with the gain and crossover settings?
I've been thinking about just getting some bungee netting from a hardware store and rigging it up with zip ties or something, might not look perfect but should work for way less than Ford's crazy prices.
I've been pulling a 3,300lb R-Pod with my 2.7L Bronco for about a year now and honestly it handles it fine, just make sure you get a good weight distribution hitch because the rear end will squat without it.
I'd go with the color-matched Velocity Blue roof - looks clean and cohesive, plus you won't have to worry about it looking dated in a few years like some of the contrasting colors might.
That 20A charge rate should be fine for a 100Ah LiFePO4 battery - most of those can handle 0.5C charging which would be 50A, so you're well within safe limits.
I'm with you on rarely taking the top off - maybe did it twice in 5 years but I still wouldn't want to lose that option since it's what makes a Bronco a Bronco.
That 0-60 time is insane for something that's supposed to be trail rated, but I'm curious about the weight too since all that power won't mean much if it's a 6000lb brick.