I have the same problem my guy, I've troubleshooted it and it is whenever for when I have created a custom scenario and then later down-the-line started the same type pf scenario but with it being labeled as a "custom" scenario. And that is exactly how it is recreated for me, pawns and loot not spawning in, exedra.

It is really annoying, is this gonna get fixed?

It is pretty easy to replicate, you only have to save the sealed vault as it is, and then go back to start your custom scenario but here is my scenario anyhow, it is pretty bloated of modifiers and stuff but they do not matter.

https://psteamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=3163008131

sorry for my late reply, but thank you!

But you understand the instructions right?
Save the sealed vault scenario, load back the saved scenario after you have created it.
You might have to backtrack to the menu again but it is really annoying how you can't create any custom scenarios for this mod whatsoever.