How to configure the system messages  url?
This issue was discussed a while ago here: https://github.com/craftcms/cms/issues/3029
As Brandon says, Craft basically has no knowledge of which site a user belongs to as they're all global.
Bear in mind that emails that are triggered from the front end will use the domain name where they were triggered from - this problem only really affects emails triggered from the control panel.
The workaround discussed at the bottom there is probably your best bet: use Twig's replace filter to dynamically replace the domain name in the link variable according to what you know about the user (in your case, their preferred language).
{% set link = user.preferredLanguage == 'en' ? link|replace('https://www.site.de','https://www.site.com') : link %}