If you play a Contact mission or singleplayer, you will see the map without bunkers, facilities, and without that silo opening.
Hadn't even thought of that! I understand the rationale behind it, but I admittedly don't like the continuity differences (which serves as a reminder that, "Oh yeah, I'm in a slightly different world").
IMO the map should always be the same in free roam and contact missions, heists, etc.--minus mobile things like yachts, whose "convenient" absence is easily plausible.
Anyway, it's nice to know that R* isn't opposed to adding new things to the existing map--I hope they do a lot more of it in the near future, as well as fixing broken map elements (nav tracks, broken ladders/geometry, heli pads that you can't call a Merryweather pickup from, etc.).