If you are working on top view maps it's a question of shadows.

A spire would be either a circular roof or some regular polygon shape, so they can be drawn using the House tool with a roof texture of your choice, on a sheet above all the other building sheets in the map so the long shadows they cast will fall over everything else. Or you could pick from the City Domes annual issue https://www.profantasy.com/annual/2018/bonus18.html which contains all kinds of small regularly shaped rooftops that could top a tall tower.

A spire might have a tall pinnacle above that roof, so you might need another sheet above that one to draw simple very thin pointy shadows to suggest that the little 'bobble on top' of a roof is actually the pointy bit of the spire.

The thing about top down mountains is that they are pretty inflexible as symbols. Hill shading means they can't be rotated or mirrored, and that means you need maybe a hundred symbols instead of just the usual 20 or so.

You might think that using a map file would be the solution, but at the current time if you have a faded edge all the way around a symbol as would be desirable for a top view mountain or hill to blend it into the background properly, the map file doesn't work properly. Faded edges upset them quite badly to the point where you end up with strange white strips of missing rows of pixels in the resulting symbol. I haven't worked out how to get around that problem myself, which is why I haven't yet done a top view overland style.

Lovely map, Prochaska :)

You could use a subtle form of coloured contour by adding a sheet with a small Blur effect on it and drawing polygons of 'Solid 10 Bitmap' fill if you feel the need to make higher altitudes paler, perhaps?

That grey overlay...

Have you considered using a nearly black one and adding a Blend mode set to Multipy and about 15-20% to that sheet?

The reason I say nearly black is because a true black one would probably interract unexpectedly with some of the dark glows. The darkest grey, or the darkest brown should be ok.

EDIT: You might also want to put a Blur on it after the Color Key and before the Blend Mode to take out any sharp edges.

I like the use of the floor textures.

Maybe put a small dark glow on those bars to make them stand up from the floor? Maybe not?