In case it was lost in the noise, an “info” page is displayed at “info.cleanapk.org”. Under Developers it has a link to a spreadsheet (ods) with API details. Under Copyright it says how to submit copyright infringement requests. Oddly for being used by /e/ - developers of “open source, privacy-enabled smartphone operating systems” - there is no Privacy Policy or statement of Terms of Service at cleanapk.
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.