I do think that having an API subset of tests is better than basing the system on all tests. Packages should have as many tests as possible, I frequently write tests which I know will break when I do further work on the code, so that I notice when it happens, and because if it happens accidentally it's probably a bug. Wouldn't want a versioning system to have a side effect of making people reluctant to write a test, because it would commit them to the results. I envision tests migrating from the rest of the suite to the API set over time.
I do like that your system completely specifies the meaning of minor and patch numbers, and wonder if there's a way to tweak my proposal so that it does so as well.