I suffered from this a few months ago as well. The space and bandwidth flatpak was taking for about 2 small cli applications was obscene. Like 30gb all because it had accumulated about 10 nvidia drivers. I found the issue on github and it was closed as intended behavior. I install alot of rust apps from source and updating them from source was faster and easier than updating flatpak just due to the overhead of maintain those drivers.
That and the fact that every app has to be run through an alias or a. overly verbose command made me discount flatpak as a serious project. You can’t ignore UX to that extent and just rely on technical merits.
Your argument seemed perfectly reasonable. I think it was just a classic case of the discomfort of someone pointing out cognitive dissonance being misinterpreted as aggression.
I do wonder if this is a case of the in-group has repurposed a word to make it more useful to them. Perhaps inside modern academia science means published in a scientific journal. Even though outside that group to use the word like that would seem wrong.