Mmm. Every time I download an ISO image or clone a Git repository, there is a record
So you are talking about the software running on the server.
Of course, it can be, but it's so easy to fix by forking that it doesn't matter, unlike with non-free software. AFAIK Pop!_OS based on Ubuntu is not spyware.
Also, Ubuntu is not free software. Only some parts of it are free.
Just a small caveat, that article was from 2012 (13 years ago). Things may have changed for the better or worse since then.