In the third place, I believe the vast majority of users don't invoke initdb "by hand" anymore. The typical scenario is to go through a packager-provided script, which almost certainly won't offer access to these additional options.
I can't speak to other distributions, but on Ubuntu pg_createcluster allows a -- followed by initdb options. So at least on Ubuntu any additional options will indeed be available to everybody. I would hope that other distributions have the same capability.
I for one would like to be able to tell initdb (pg_createcluster) what to put in the first column of pb_hba.conf in the same way I can already use --auth{,-host,-local}= to set the auth-method column. Ideally, for simple situations (think testing scripts and the like, rather than long-term installations) the pg_hba.conf could be created by initdb and not changed after that.