At least from what I can find, here's the original version of the changed snippet [0]:

    let date_source = if let Some(date) = matches.value_of(OPT_DATE) {
        DateSource::Custom(date.into())
    } else if let Some(file) = matches.value_of(OPT_FILE) {
        DateSource::File(file.into())
    } else {
        DateSource::Now
    };

And after `-r` support was added (among other changes) [1]:

    let date_source = if let Some(date) = matches.get_one::<String>(OPT_DATE) {
        DateSource::Human(date.into())
    } else if let Some(file) = matches.get_one::<String>(OPT_FILE) {
        match file.as_ref() {
            "-" => DateSource::Stdin,
            _ => DateSource::File(file.into()),
        }
    } else if let Some(file) = matches.get_one::<String>(OPT_REFERENCE) {
        DateSource::FileMtime(file.into())
    } else {
        DateSource::Now
    };

Still the same fallback. Not sure one can discern from just looking at the code (and without knowing more about the context, in my case) whether the choice of fallback was intentional and handling the flag was forgotten about.

[0]: https://github.com/yuankunzhang/coreutils/commit/850bd9c32d9...

[1]: https://github.com/yuankunzhang/coreutils/blob/88a7fa7adfa04...