The efficient alternative, which I’ve seen used a few times in these cases, is to retcon a high-quality fake history into the source tree after the design has stabilized. This has proven to be far more useful to other engineers than the true history in cases like this.
Incremental commits are nice but not all types of software development lends itself to that, especially early in the development process. I’ve seen multiple cases where trying to force tidy incremental commit histories early in the process produced significantly worse outcomes than they needed to be.
I agree that one can do good commit messages also early on though. Initial commit can be "project skeleton", then "argument parsing and start of docs", then maybe "implemented basic functionality: it now lists files when run", next "implemented -S flag to sort by size", etc. It's not as specific as "Forbid -H option in POSIX mode" and the commits are going to often be large and touch different components, but I'd say that's expected for young projects with few (concurrent) contributors