Remove instances of `prometheus.DefaultRegisterer`

Proposal

Following #12549, the scrape and discovery packages no longer require use of the default registerer. However, prometheus.DefaultRegisterer is still used in the codebase, particularly in main.go. It would be good to replace this with a single prometheus.NewRegistry().

This would have a few advantages:

• We are closing a loophole where a new feature could still use prometheus.DefaultRegisterer outside of main.go.
• It's a signal that prometheus.DefaultRegisterer is no longer required.

While I think that scrape and discovery packages would work well with a non-default registry, there could be other packages which still rely on the default resiterer. We would need to take extra care when doing this change:

1. Browse the codebase for code which registers metrics in the default registry
2. Run a Prometheus instance which uses these bits of code.
3. Reload the config of that Prometheus instance to make sure there are no errors due to double registration.