Doing a ActivatePersistentLevelTemplate(a34ed151-af71-4f09-9d28-f1f00e914506); on the "main level" seems to make the story goals respond to the intended objects, so it indeed seems to be the way to go! I'm still a bit vary but with this, I'll proceed with working as I've done so far, and should it not work out in the end for what ever reason, it's just a massive chore of combing through everything with a find & replace job, which in worst case is a good dual-monitor Netflix bingewatch excuse to combine with.
Thanks for your feedback Windemere, it seems like it's what I need to do.
