Hopefully removing the roof rack isn't too big of a deal. Think I saw somewhere it's just a few T30 bolts. I don't plan on using my roof rack often other than shuttling my kayak to our beach, so it will be off the majority of the time.
You can take off front panel with rack on. If you want back panels or whole top off, the rack needs to come off. Looks fairly straightforward in the video I saw. Can’t find it again though.
Roof racks and (factory) rails both need removed to take off the top. And you cant have the roof racks or rails without the top on. You can download the owners manual which explains how, with pictures, to install/uninstall roof rails
Some aftermarket parts maker may find out a way to have roof rails/racks on without a top.