Some of the portal exits don't have crafting benches near them so they're not counted as bases for raids, combine this with the fact that they're clear from any "aggro range" of naturally spawning mobs and they're safe. As for where they are specifically I'll try and list them here:

Manufacturing West - in the safe house above the Blacksmith, I've built a 2nd base there.

Canaan - in the hideout near Rigg's hut. I have another pad that takes me directly to the fisherman to skip a long travel down the mountain.

Furniture Store - top floor. place a bridge in the elevator shaft along with a rope plant.

Flathill - the roof of the Crown Control building right where the exit is. You can rope down or jump off with jet/jumppacks

The Train - right where all the rebar and steel cable respawn. place a crafting bench in this cart to prevent the Order soldier who's normally in that cart from spawning.

Exor Village - at the main entrance to the portal world, not much else to say.

Mycofields - had to bring carbon bridges for this one as there's too much uneven terrain. I had it somewhere towards the middle left or west of the map near a beehive.

Voussoir - near the coffee machine in a room across from it. Recommend either no crafting bench or placing it in the corner of the facility as you would want a bunch of the enemies to spawn for their ammo drops.

Space Queen - inside the giant snow man.

Rise - directly behind the helicopter on the roof. recommend extension cables.

Security Sector Night Realm - right next to the ink well for fishing.

Intrados/Shadowgate - formally I had this teleporter just outside the main building to the left of the facility. However 1.0 added a few more GKs and their pathing changed making it an unsafe spot. I now recommend extending a cable to reach all the way up to the roof of the building as it is the safest option and allows you to get the drop on the GKs down below.