No, you're not overthinking it.
YJs were confused at the factory, with rounded hard top door openings and square soft top door openings. (evidently the hard and soft top teams weren't talking).
Plus, the upper doors made for factory half doors can be different than upper doors made for soft lower doors (Supertop doors).
Read thru this Doors and Windows
page on our site to see what is designed for YJs. We make uppers that will fit the factory hlaf doors, and we make uppers that will fit the soft lower doors. (and there are a few competitors out there too who have options).
The smartest thing to do would be to get your lower doors first, then solve the upper door problem. Because you're also going to have trouble finding steel lower half doors at this point, too, so you may end up going with full soft doors. Or a different solution altogether, like our Element doors.