There might be other glitches that cause a similar outcome. But every time I tested this with a clean Documents folder before, the items that were categorized as the base game were exactly the same, which is also what caused me to think this issue only happened to Store items that were patched. But like I said there could be other similar issues with this as well. For example, in my game, objects from the Town Life Stuff have the icon of Outdoor Living Stuff, but the filtering works correctly so I don't mind it that much.
I think in the future, EA might need to update TS3 to work with the new EA Desktop client considering how integrated TS3 is to Origin (they can even hide games with illegal CD keys from the launcher). This is obviously speculation on my part, but if that happens I will push this issue forward so that we can get this fixed while there are some devs around. The game already puts some random *.mp3 files in the Custom Music folder in the Documents, so they might as well put the ContentPatch.package in the correct directory in a similar fashion. If an update happens, hopefully they will fix this considering this appears to be a post 1.69 issue, and they fixed CAW before, which was also bugged post 1.69. If they never need to patch the game or something, at least the issue is not game breaking so it is fine.
To @mate54 , I remember encountering a similar issue, but it has been a long while since I encountered that. And I remember that fixing itself when I clicked to a non-UI place in the game. But that might be a totally different issue. And I don't really use the sort by room in buy mode which is where the featured sets thing is in, so I sadly can't be of help there ☹️