It changes for a good reason. The results are narrowed down, and so are the tags in the filter because there’s no point in showing tags that wouldn’t show any results.
It’s exclusive tagging: we only want to see results that contain all selected tags.
The Tags Filter in DEVONthink works this way, too.
This organisation of tags into groups is a good thing. Tags represent different things, and it makes sense to separate the concepts into groups.
Also, the tags that represent the type of content and the consumption status can be set up in the beginning, and from that point onwards, the only new tags created over time are Topic tags, according to the item being saved.
But it’s even worse if you don’t have groups at all to separate the tags, because that actually means that you actually have them all in a single group.