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The taxonomy module example shouldn't exist in its current state, it was ported from 7.x which was similarly broken. I opened π Deleting a vocabulary will fail when there are lots of terms Active to change it to match the content type example.
Eventually, we could add batch/queue support for deleting unbounded numbers of the same entities, but until we have that, we shouldn't be attempting to load and delete potentially millions of entities within a form submission.
I think this is more of a plan (that could have bug reports as child issues), but agreed it's a problem.