@AdrianVovk I can elaborate my earlier answer just a bit.
1. SSH service can be enabled from GNOME settings.
2. Network settings can be changed from GNOME settings.
Security-wise both are potentially much more destructive actions than let's say allowing app to access home directory files.
I'm not sure what you are referring to on asking permissions but I have never encountered a Flatpak app that would do that. E.g. in order to use a Matrix client I sometimes need to save or upload files. Without using Flatseal it simply is not possible.
In my iPhone the app both asks permissions OR I can enabled/disable them explicitly from settings. I don't really think this is too much robustness to ask but obviously it is in the end the choice of those who develop GNOME.
Just my silly opinion I guess...