In addition to f-droid, e’s other source for apk’s is apkpure.
My guess is cleanapk does not store copies of apk’s, and only keeps pointers to download links for the apps app, but it’s not confirmed.
For details on how the apps app works with cleanpk, the source is here:
PS. There was a problem with accounts being locked, and unable to reply; otherwise this reply would have been much sooner.