Lots of vastly different maps from different mappers with different ways of approaching things, that is one of the things that make the atlas (and the competition) great. I love all the great variety of the maps in the atlas, some focusing on visual looks, others on accuracy and yet others on the story they tell.

The annual isn't intended to just be 12 issues of new artwork. As stated on the product page:

While maps are not the most common of issues, if you look back at previous years, you'll find that there is indeed a collection of various map issues sprinkled among the years.

Different kind of issues bring different values to different people. A nice map with a detailed description is great for improving one's map-making skills and learn new ways of doing things, and may even be used as a ready to go map for an adventure.

Wyvern is correct here. Basically, anything you can do with a symbol inside CC3+ is completely fine.

You're only running into problems with the atlas if you are doing anything to the actual .png files on disk, which includes copying, moving, renaming or modifying them. Also, if you import images as symbols into your map using the Import pngs command, you can only import images from atlas-legal sources in their original location, and make very sure NOT to check the "create other resolutions" or "copy to folder" options while doing so.

They're not approved for the atlas.

The main reason for this is that they lack proper CC3+ integration and symbol catalogs, meaning that while they might be free, it is hard to use them in a consistent manner that will let other users use maps with these symbols in them.

That's completely up to you.

The main thing I very strongly encourage when making a non-overland map, is that there is a symbol (or equivalent) on the parent map to link it to. No making an inn and linking it to a blank spot near the road on the parent map because "there could feasibly be an inn here". It is the mappers responsibility to place interesting places in their maps for others to link from, and if no marker for such an interesting place exist on the map, well, then an intermediate map may be required. So generally, the idea with an intermediary map is to make up for "shortcomings" of the parent map.