Many web clients have chosen to default to trust stores within their own ecosystem for usability and reproducibility reasons. When I as a user run "pip install requests", I expect to be able to issue HTTPS requests. I do not expect an implicit system dependency on ca-certificates - that might not even exist on my system!
If you want all of the web clients on your system to use a centrally managed trust store, then it's your responsibility to (a) know and enforce what clients exist on your system and (b) configure them all to use that trust store.