I can't find the relevant discussion thread at the moment, but I believe this was because the default configuration in some shared hosting environments would have allowed users to receive certificates to others' websites.
Edit: https://mailarchive.ietf.org/arch/msg/acme/B9vhPSMm9tcNoPrTE...
[edit] This also means I should probably make a PR for automating DNS-01 with my DNS provider (he.net).
However, plugins need not live in the main Certbot repository. Maintaining a plugin yourself may be the lowest-friction way to build one right now (or may have its own challenges; I haven't tried that approach).
Lexicon supports he.net[1] and Certbot provides a class for building Lexicon-based providers[2] with very little effort (although perhaps more effort and duplication than would be ideal[3][4]).
0: https://github.com/certbot/certbot/issues/6504
1: https://github.com/AnalogJ/lexicon/blob/master/lexicon/provi...
2: https://github.com/certbot/certbot/blob/master/certbot/plugi...