Yes. Just pick the CA Pro template instead of the CA3 template. Or for a full selection of the old templates, use the "Pick a pre-defined template" option in the first step of the new map wizard, then in the template select box, hit Select Path and navigate into the CAPro folder and into the desired subfolder, pick any of the templates and hit ok to preview them all in the template picker dialog.

1/2. No. It only lists bitmap fills in use by entities. But, keep in mind that the fill property is defined on all entities, whether they use it for anything or not, as fill is one of the basic entity properties. So for example, a symbol reference do actually have a fill defined, even though it will never use it for anything. But my command can't know that, so it will include the fill in the list it uses to determine which add-ons are in use.

3. Use the IRD command. It will list the actual file names of everything. You may still need to to some searching because it can't pinpoint the entity in the map, but knowing which file is being referenced usually helps you work it out.

Notice that navigation link that leads to a dungeon in the top of that section?

The current linking location doesn't work too well, since there aren't really a feature marked on the map for it.

So it would be great if you put in a symbol in your map for it so I could link to it from there instead of from the continent map like it currently does. This could be a symbol on either the main map of the area, or even better, on a lower level map if you make a more detailed map of the areas as you often do.

As you can see from that map itself (https://atlas.monsen.cc/Maps/Dungeon%20Of%20Ice%20And%20Fire), the entrance is a cave opening, so some kind of cave symbol would be great.

You are using the wrong drawing tools for the style. The map you are making is in the Overland Mike Schley style, but your drawing tools have been set to overland CC3. Change the drawtools style, and it will work as expected.

The reason this happens is that fill styles are defined in the template, and those drawing tools are trying to use fill styles not defined in your current map, because they weren't made for that one.

(If you really want to use those drawing tools, check this FAQ entry.)

My keep right here is essentially a multi-floor perspectives map (needs some zooming in):

Do note that it can be pretty confusing handling the floors. While it is perfectly doable, Perspectives itself doesn't really know what a floor even is, it just works with surfaces. It is up to you to position those floor surfaces to make the illusion of floors look right.