• Yes. Anything you do in-map (using allowed resources) is perfectly fine. The main thing here is that you cannot find your own symbols/fills from outside the allowed resources, because this causes distribution problems for the atlas.
• Yes, that is fine.
• Yes. I usually prefer to have these on different maps, because CC3+ can really only maintain one scale in any given map file, but there are cases when things work best together.
• Nothing against tokens directly (as long as they adhere to the allowed resources), but generally having monster tokens on the map makes the image export a bit weird, anyone downloading just the png file from the atlas would have a image file with immovable tokens.

Am I understanding you right here that each sheet is one floor, so that all the floors are in the same map file?

In CC3+, because of things like sheets effects and such, maps tends to use a lot of sheets, so it is generally better to use one map per floor. Although it is possible to keep it as one map too, but then the macros hiding the sheets must be updated to hide the complete set of sheets. With some nice naming you can do this rather easily by taking advantage of the HIDESHTF and SHOWSHTF commands which hides and show sheets by a wildcard filter, so for example all sheets for floor 1 could be named FLOOR1_SOMETHING and so on.

That would be my preferred solution for the poles, yes.

I really loved the map showing all 7000 of the rivers feeding the Mississippi. Kind of cool how it collects water from a really huge part of the US.

Well, that's the problem then. Just move the COASTLINE sheet upwards to right between RIVERS and ROADS, which is where it is supposed to be.

What probably happened here is that the COASTLINE sheet was missing from the template you used, which caused CC3+ to automatically created it when it was needed for that outline. But CC3+ don't know where in the order to put such a automatically created sheet, so it just puts it on top of everything.

Edit: And a fast Lorelei sneaks in......