It's trolling of the "everything new in Linux is crap" type, just check their post history. Random data loss because one uses Flatpak, seriously?
I wish I was joking: https://twitter.com/planner_todo/status/1492084099875586049
Try again.
Both of these things can be true at the same time: The library authors ultimately messed it up and could have prevented it by reading documentation better. Flatpak has a footgun and could have prevented it by better dev UX and/or structuring docs differently.
Hopefully this incident is leading to improvements in both.