> icons from the previous run are still visible in the tree tab even though they don't function.
Well that's a bugger. I thought we fixed that bug
> Are the different characters really any different?
They each have their own special trait that has a lot of recipes attached. Most of them are just text but a couple have mechanical effects as well
> I really have no idea what to try to reach the two other endings
Have you found all the locations? There's one ending in the river location (it should be fairly clear how to reach it once you look at the traits there) and you can get another ending by exploring some more after unlocking the river location (in fact, there is a quest that tells you to do it).