Hiya @egli !
Thanks for posting it on GitHub issues. Please share the link so others discovering this issue can upvote it or see the progress on it.
Currently there's no way to limit the inputs on the default select box.
Two options.
Since you are using a custom form, you could create your own select list with just the languages you want to support.
Store this to a different value (user.data.custom_preferred_languages). You could then set up a user.create.complete webhook to copy the value of user.data.custom_preferred_languages to user.preferredLanguages`. That way this language will be used in the future. (The initial email won't have that info, however).
Another option would be to have a javascript function that would run whenever the user.preferredLanguage select box is displayed, and would trim the values down to what you desire.
I realize this isn't the smoothest, but it should get you the control you want.