I have noticed that what you call "fog of war" isn't saving even in the same session. You can start in Atlas Park, run up to the monorail and go to Kings Row. Then take the monorail back to AP and the fog has returned covering everything that you uncovered earlier.
Yeah, that's expected. The client only has a single global map state, so it resets every time you change maps. The fog is either saved/loaded to a VisitedMaps file (for static zones), or sent by the server for a mission map. Everything in Paragon Chat is a static zone, so it's up to the client to persist the fog state.
As for the marker in Breakout, I seem to recall it was visible on the floor next to the drain. I didn't see it when I looked for it, although I found the two most common - one on top of Atlas's sphere and the other next to the flag on top of city hall in AP.
I took a look and it's actually flipped upside down and embedded in the ceiling in the corner; and not visible from inside the cell. That's probably because the volume that triggers badges being awarded (a large cube) is attached to the marker, and that was the only way to keep it from overlapping the adjacent cell.
It's possible the version of Breakout from the Ouroboros flashback mission - which uses a different map - had a second copy of the marker geometry placed manually in the cell. PC uses the original from the tutorial, however.
Maybe you could make it so clicking on the door of the ship teleports you to Mercy Island. I assume you had to do something like that to get all the other modes of transportation working.
All of the direct transport links already existed in the map files; Paragon Chat just reads them and processes the instructions contained in them. I didn't manually assign each one. IIRC, the flier door never took you to Mercy; it was the pilot NPC standing next to it who teleported you there after completing the mission, similar to Coyote.
Galaxy City ( /mapmove 29 ) bug(s):
It's not listed as Echo Galaxy City, just Galaxy City
That's intentional. Galaxy City was one of the biggest roleplay spots in the game, especially for EU players. And since the primary use of a chat client that doesn't have combat or missions is RP, it made sense to restore it as a primary zone. However, there's still some known issues with it.
Also, the map that PC uses is not the Echo: Galaxy City map, it's the actual Galaxy City map. When the Echo was created, a copy was made of the zone for it. Among other things, the arena doors were disabled (you'll notice they work in Paragon Chat). The actual Galaxy City zone had its major NPCs deleted, but was otherwise left intact so that characters who had logged out there would not be trapped, unable to log in. They put in an instant teleport field so that any character who logged in to Galaxy City would be teleported to Atlas.
At some point, the teleport field broke or was removed. After that, there were several ways to get to the real Galaxy City, which was separate from the Echo.
1. Have an old character who had been parked there and not yet logged back in
2. Have an old character who had been parked in Outbreak since before the new tutorial. Complete the old tutorial and select Galaxy City as your starting zone - you would be sent to the real one, not the Echo.
3. In an SG base, the arcane teleport beacon for Galaxy City was overlooked and still pointed to the old one (the tech beacon had been changed to go to the echo). This was eventually fixed, but for quite a while this was the easiest way to get to Galaxy.
4. Use the Long Range Teleport exploit to teleport directly there using the mapmove number for it.
You can take the monorail to Galaxy City (I tried it from AP and KR), but not out (the monorail doesn't even show up on the map and you can't use the monorail in GC). When you go there, you're dropped at the tunnel from Kings row (and taking that tunnel takes you to the monorail station in Kings row). However, the tunnel from Kings Row to Galaxy City is blocked off. If you can take the tunnel to Perez Park (it drops you in the middle of PP), but the tunnel to GC from PP is also blocked off.
All known issues due to the devs deleting the destination beacons (and the door beacon that makes the monorail work) from the Galaxy City map when they disabled it. It's on my wish list to restore those beacons, as well as the missing NPCs, from an old copy of the map in order to undo the damage, but it's deferred until there is a cleaner way to patch it in.