When we added support for ssh, we very explicitly discussed that we need to be careful on which services we hand off control. The reason isn't simply being in control, but rather that those are implementation details that the system will rely on and may break in strange ways during future updates if every device has a different behavior. That's why we rolled back the changes you did without discussion and reviews, and that's why I invited some discussion on the topic before landing that PR.
So, with that background out of the way, let's see the specific cases.
Why do we have that on today? The reason people are asking for it to be disabled in the local system seems to be a good reason to have it always disabled. We don't want systems dying because their disks are full of logs, and we already have a daemon that does exactly the right thing, offering access to the latest logs.
The bug you link to is asking for the NTP server address to be manageable, which is sensible, not for it to be disabled, which is dangerous. Ubuntu Core systems rely on signed certificates which have timings associated with them in multiple cases (TLS, assertions, etc). A system with a broken clock that can't ever synchronize its clock will very likely be bricked until it's logged into.