I thought it might be even simpler than that. (I thought maybe it was map objectives that weren't there) I ended up with more questions but here's what I did (i'm including the map files I loaded so you can replicate the results for yourself):
It occurred to me that there were mission maps that were all single level and were unique to certain missions. For example, Faultine Dam interior (MAPS/MISSIONS/UNIQUE/FAULTLINE/DAMLIES/DAMLIES.txt) and the abandoned SG base
(MAPS/MISSIONS/UNIQUE/ABANDONEDTECH/ABANDONEDTECH_15/ABANDONEDTECH_15_LAYOUT_01_04.txt)
where you pickup Doc Delilah are only used for very specific missions. They aren't randomly assigned. Also, they do not have multiple floors. But no mini maps appeared when I loaded them.
Then I loaded Bunker (MAPS/MISSIONS/UNIQUE/BUNKER/BUNKER_01.TXT) and the Mini-map appeared and worked as normal!
Further, it isn't just the fact that they are mission maps. Because outdoor mission maps load the mini-map and FOW works just like it should. The winter event (MAPS/MISSIONS/UNIQUE/WINTER_06/WINTER_EVENT06_CROATOA.txt) and a Mercy factory mission map (MAPS/MISSIONS/OUTDOOR_MISSIONS/V_OUTDOOR_MERCY/INST_FACTORY/INST_FACTORY.TXT) worked as well.
So it isn't clickable objectives or multiple floors that are the problem since Outdoor mission maps have clickies and the maps I loaded were single floor.
So what does it mean? First, I think that the reason some work and some don't is because of zoning. Even though they are mission maps, the outdoor maps are treated as separate zones. (Can't explain "bunker" unless it is also technically a zone like Pocket D)
I think the key is Door missions. Because when you click on the door, you don't leave the zone that the mission is located in. So when you are inside the mission, you were still connected to the zone you were in.
In Icon, you are not connected to any other zone because you don't have the mission parameters that tell the client what Zone the mission is in or where the doors should dump you if you leave by them.
Indeed, using Noclip, if you leave a mission map, even one that only appears in Faultline or the Hallows, all you get is inky blackness.
So I go back to my original theory that is the lack of mission data (server side) that is keeping the mini-map from appearing. Since there is no Server to keep track of where you are in the world and that is connected in some way to when/if the mini-map is displayed.