As for number 1, I can confirm that this is definitely available now. I'm currently running an overland hexcrawl type campaign. I've got my map created in Hexographer, and as the PCs uncover hidden elements, I've been adding icons to represent the locations.
I'm keeping the master map as a Hexographer project, and between sessions when they find something formerly hidden, I go into the project and add the element. I then output a .png from the project, and as long as the resolution is identical to my original map output, I can change the image in the smart image snippet, and it keeps all the reveal masking and pins in place. I've done this at least five or six times already, and it works like a champ.
As for some of your other points, I and others have also requested more customizable pins. The argument is the pin color chosen came after a lot of trial and error for visibility and such (which I see). There has definitely been mention of this, and my understanding is that more flexible pins and/or icons are on the roadmap, but my guess is they're pretty far down the list given the other big things on LWD's plate (content market, web client, calendars, etc).
Also, the idea of additional layers on smart images has come up, and it is my understanding that this is also on the roadmap. That would probably get you a lot of what you're looking for with things like revealable political boundaries and the like.
Some relevant threads:
http://forums.wolflair.com/showthread.php?t=50292
http://forums.wolflair.com/showthread.php?t=49096
http://forums.wolflair.com/showthread.php?t=51514
http://forums.wolflair.com/showthread.php?t=46876