About a month ago a posted a concept drawing showing a removable soft tonneau cover for the roof:
I tried the tonneau from my Jeep-tub trailer on the mocked up Safari Cab parts to see what it might look like. This tonneau is a little too wide for the JK hardtop, and in the photo it's just sitting on top - in actual use the tonneau rails would be bolted to the top and would conform nicely to the curves of the top, but this gives a pretty good idea of what it might look and how it would compare to the factory top - it's pretty flat so it wouldn't look very different...
Without the tonneau sitting there, you can get an dea of what the roof might look like with just the rails in place. Again, this set is too wide for the JK top, and they'd be bolted in place to conform to the curves on the top. When the cover was off you'd have a full open roof.
The rails would be removed when the hard roof panel would be installed.
I've run hundreds of miles in the rain with this tonneau on my trailer, and it's been completely weatherproof, so I think something like this would work out very nicely on the hardtop.
When I get to the appropriate point in the project I plan to have my friends at the tonneau company make me a tonneau custom fit for this application to do some testing.