F-Droid builds with the needed tools. If you use gradle flavors that's up to gradle to do its own thing. Analytics are a different topic, but yes, usually flavors are used to separate the fully FOSS build for F-Droid from the other variants.

Specifically, I was curious if it was possible to publish two completely different apps from the same repository using two build variants. The specific case is my child tracker app (https://f-droid.org/it/packages/it.danieleverducci.lunatracker/), I could very easily add a build variant to create a pet tracker app: just change the package name, app name, icon and the type of trackable events, all the rest of the logic is the same.
I imagine in this case I should create two different entries in the F-Droid metadata repo. But how can I tell it which build variant to build? And also, is there a way to differentiate the fastlane data for the two apps?

We have some of those too, but the discussion is longer, let's switch to https://gitlab.com/fdroid/rfp/-/issues instead.