For sharing, yes, it is completely fine. The only things that matters when sharing the file is that the recipient have the actual art files on disk. You can make as many fills as you want inside the map without that being a problem, sharing issues only becomes an issue if you manipulate the png's on disk (such as making copies of them). As long as you can see inside that fill style dialog that both versions point to the same png files, then everything is fine.

Looking nice. I like the way you place man-made structures.

I like the more natural feel of the map. I think it works better as a computer game map as well with the zones not so obvious. They're still there, but more blended into the map. And whenever a pure zone-map is needed, it can be handled by border lines or overlaying partially transparent polygons to introduce color variations.

Sounds like an interesting idea. While I have no idea if something like this will be made for CC4 or not, you can already today get access to all the data needed, so that should be able to be done with an add-on, meaning even if it isn't put into CC4 by default, it should be possible to write for anyone with a bit of programming experience and put in without PF having to add anything to pave the way.

This is more or less what I am doing in my dynamic dungeons project. Unfortunately, I haven't been able to pick it back up in a long time, but it still exists as a proof of concept for this functionality. Hopefully I can finish it one day. There is a video showing it in action linked from the beginning of the article:

If you name them sensibly, you can achieve the same (But you do need to use a command, not the GUI). Say you have a bunch of layers with different kinds of GM secrets, then you can simply name them GM Secret Doors, GM Secret Traps, GM Secret Secrets, etc. Now, you can toggle the visibility of all of them with TOGLF GM*, with the companion commands SHOWF and HIDEF. ('F' here means 'Filter').