The vanilla tag overrides only serve the purpose of adding ThemeTags with ThemeRepeatDistances to certain types of POIs in an effort to prevent things like neighbouring celltowers, book/hardware stores, prison, gas stations, etc, sometimes extending vanilla ThemeTags sometimes creating new ThemeTags to fit PEP similarities in theme compared to vanilla. I wouldn't remove them. They also make sure no fake traders spawn next to real ones which would look bad ingame / increase ThemeRepeatDistance for traders a bit because 40 traders on a 6K map is ridiculous, this forces the traders to spread out more.
The PEP rwgmixer has been simplified recently in terms of prefab weights and next PEP update scheduled later today fixes an xpath error on my part in the prev version. All it'll try to do is encourage 1 of each prefab to spawn though it currently does have a bias towards higher tier POIs due to those scoring higher and I'm not sure if I should try to compensate this with +1 bias to T4, +2 bias to T3 etc etc. I'm curious how you'd feel about something like that to decrease higher tier weights @zztong?
Besides that it increases the countrytown/town/city counts on most map sizes and tries to optimize size brackets some by changing those up a bit.
With regards to Teragon, Zephyr created a PEP POI list which should be included on next update. I also heard rumors that Teragon might be able to simply load POI folders itself in the future.