I just noticed that native launcher on Mac OS (and I slightly remember to have seen this on windows as well) does not make some older versions run in the directories set in a launcher profile. Instead, all data goes straight into normal Minecraft directory. This seems to happen for every version without the internal server model, but definitely all beta versions of Minecraft.

I noticed that this is not a problem on my linux system though. The launcher here follows all settings and beta versions are run in their distinct directories.