I think there's a middle ground. Sure, a single crontab makes it hard for packages to schedule things and makes it hard to assign ownership to individual packages/people/whatever. I can recognize that, and how it would be a problem for a large enterprise or even just for software developers who want to bundle some kind of cronjob with their package.
What you could do instead of a crontab is have one folder with a bunch of services/timers in it, where each file represents a single service that needs to be run. It would mean that you can still understand all of what's going on timer wise by looking carefully at one source, but you can still assign different services/timers to different people/packages/organizational-units/whatever.
Splitting each individual cronjobs into 2 different files is just crazy from where I am. Like you already have a bunch of different service types, at least give us the option to use a "periodic-oneshot" service type instead of this craziness. There's no need to have different packages/people responsible for a service and its timer, and if there is some edge case where it is you can still have ssperate timer services just they can live in a separate periodic-oneshot service file and use the original service as a dependency.
There's separation of concerns and then there's this. Take any principle too far and you get some craziness, and systemd has most of the infrastructure needed to solve this in a much more elegant way. Like at some point it has to just be bad design and not just different priorities, right?