Sure, they ask and put it in your profile. Then when you get to your cabin, you can ask the attendant to separate them. The default is together as cabins are made up quickly the morning of departure day.
Allowed gaming the system is still gaming the system. If you book a guarantee, keep it. Don't make someone who books later and pays full price take that connecting cabin
I got the 50ish when I searched all 14+ cruises on Royal from/to anywhere and subtracted all the 14 night ones. If your lower count makes you feel the thread doesn't matter so be it.
Similar to our experience. For many years we go to Maui on vacation, so left the ship in Honolulu and spent several days sightseeing there before flying home. We also enjoy the sea days. In fact we did a B3B on Explorer last January and never got off the ship. We've been to all of those Caribbean ports many times and prefer to enjoy the quiet ship in ports.