I'd like locations books... fold out or at least full page maps on the right page with the left page having descriptions of characters there, plot hooks, modular ecounter type stuff, etc. Or one every 4 pages be the map. Chapters sorted topically. For example cantinas, city/town maps (doesn't have to be a whole town just a small part of it so it doesn't define everything, not all the buildings have to be labeled kind of like the most shutta map in the beginners box), temples, ships (deck plans like the krayt fang those could be two pagers for silhouette 4 ship)
Edit: actually organize those by town (withe character information plot hooks in the front along with a town map, and maybe 5 buildings in the town map getting their own on page map. The ship chapter could be a space port showing a bunch of docking bays maybe 10 or so (with ships 8th them and stats write up for the ship in the corners of the two page spread) maybe a cantina, a few other buildings getting their own on page maps.
The reason they don't do this is it is VERY resource intensive especially if you need to re edit the map for any reason and then need to re edit the text that goes with it. and it is less universally useful. And if the map is of a known place it cannot change and might make a mess of what the GM was doing before the book came out. Expect very little in the way of maps. They will be made where they are useful. Mostly in Adventures.,
The point of the proposed format (proposed in the edit), map of a town or a small portion of a large city, with only a few of the buildings labeled, and only a few of the labeled buildings getting separate interior maps, is so the GM can make a purpose for most of the buildings and the rest of the large city is not described and can be anything (i.e. it was something previously off camera). Similarly the purpose of the text describing the maps/adventure being in the first few pages of the chapter, is so that it doesn't have to be right there. The docking bay/ships maps are an exception in that the stats and description of the ship are written in the corners of the page(s) with the ship's interior map. For the most part, those ship descriptions would NOT mention an owner. So I think this (revised proposed) format addresses 95+% of the possible conflicts that you mentioned.