We are also still trying to figure out how to mount sea kayaks on the roof and still be able to have solar panels. Not an easy task but we are trying to get creative.
It's a little harder with kayaks than with surfboards, but I faced the same issue in wanting to bring shortboards and longboards on the trip. What we decided to do was to build a safari roof with pockets for the surfboards, and then mount the solar panels on top. Its basically a faux roof that sits 5" above our actual roof, with dividers for 3 longboards and bags. Its makes us 5" taller, but it has myriad benefits. I essentially have the equivalent of 6.5" of foam insulation on the roof, not to mention the reflective mylar coatings of the board bags. It also gives you the full roof square footage x2, one set for solar panels and one set for stuff. In your case, the downside would be the increased height in dealing with kayaks, in case you could see situations where you didnt want to travel with the kayaks. But if thats not a problem, or the kayaks will always be there, the safari roof adds a lot of insulation and heating/cooling protection and a lot of storage. It also adds structure to the roof if you are looking at doing a pop top or the like.
If you go with the half hexagon shaped roof you showed in your earlier drawings, the kayaks could go on either side on the angled portions and then have a flat safari roof spanning the whole roof. So you'd have two angled pockets for kayaks, and what amounted to a mostly flat roof in terms of total height. It would minimize the max height gain and allow full roof solar excepting skylights and vents.
The other thing to maybe consider is doing away with the fixed bathroom walls. Its an intimate space to begin with, but it creates such an open feeling to not have them there. We have ours on a slider which goes into the shower bay, so that you can deploy the shower curtain if the need arises. No aural privacy, but some visual.
Stoked to see this all come together. Hopefully we can meet at expo next year with completed rigs!