I believe that this comment and the link are critiques of the host and not the named projects (excepting maybe Access Dots, which OP has noted as closed source but plans to block from network) or the guide itself. If that is the only concern then, at best this comment and the linked critique are unhelpful because they are conflating the hosting sites’ goals with each project they host or the guide as a whole.
It would also seem to affect a relatively small portion of the guide. Skipping Aurora Store (and thus Access Dots), the APK sites, and replacing the gitlab firefox repo by installing Klar and Fennec from F-Droid would seem to address the software concerns raised.
Can you elaborate on this being bad advice?