Even if all applications look at the OS trust store, in my experience there's always a gap distributing the CA to every consumer, leading to time spent on debugging from time to time... Maybe that's not the case in perfectly homogeneous or sufficiently small environments where every team uses the same infra / stack.

It's hard to get right when OSs, programming languages, browsers and sometimes other applications have their own opinions about trust stores. I understand why our IT department want corporate devices to use internal CA certs on paper but it just breaks stuff in the real world.