This pinpoints the major problem exactly. Without dependencies between PRs there's really no sane way (with this feature enabled) to submit a series of commits while expecting those commits to remain separate.

Oh, and I object to the general sentiment in the responses to your post that seem to value drive-by/inexperienced contributors over the "experts". Yes, we definitely should make things as easy/simple as possible for new contributors, but NOT at the expense of adding a gotcha for expert contributors. The experts are what keep a project going over many years instead of just releasing version upon version of trivial spelling fixes.

(And, btw, the default "merge" option for GitHub PRs also sucks. It should be possible to simply disallow non-FF merges and to force all merges to be FF. EDIT: Interestingly, this seems to be about the only workflow explicitly forbidden by the new rules... unless, of course, you're willing to merge everything manually using your local copy of the repo and pushing from that to GH.)