Seems very reasonable, from my use. I commit much more often, as checkpoints, with branch rules that prevent force pushes/deletions, so the agents can't delete anything. And, suspect MS is only counting commits, and not the eventual squashes to one commit.

And every checking runs a whole CI run?

We had it internally with our teams that open a PR to then push like 10-20 more commits but never actually interested in the client builds etc. turned out they opened the PR as a checkmark/ way to share the current state. We set cooldowns and auto cancel for the ci. And then there is the developer who uses the CI compute to run tests instead of running them locally for various reasons. We had to remind that compute isn’t for free.