There's a middle ground though: rebase your commits, but not necessarily into a single one. Before I submit a PR, I rebase my branch (which has lots of small commits, some of which undo previous work or are a work-in-progress), and make sure that every commit is as small as it can be without including work that is halfway done (so all tests still succeed), and have a clear description of what they're doing.
I then have both a nice history, and I can bisect to find a problematic commit, or inspect the commit history of a single line to get more context about it.