The case for it is where it's not easy to plop a file in a .well-known path on port 80/443. If you have a reverse proxy that is easy to set up to publish that, that makes it easier. I guess I could have used different wording, I do consider making the .well-known available a subset of hijacking the port, but can see why it would be confusing. ACME setup can still be trickier to set up, but is definitely a good solution if it fits in your environment.
(You say hijacking the HTTP port, but I don't let the ACME client take over 80/443, I make my reverse proxy point the expected path to a folder the ACME client writes to, I'm not asking for a comparison with a setup where the acme client takes over the reverse proxy and edits its configuration by itself, which I don't like)