Flatpak and Electron don't sabotage any of these things. Flatpak usage is entirely orthogonal, and Electron actually has best-in-class accessibility, i18n, text rendering, keyboard navigation, RTL support, hi-DPI support, etc.; its widgets feel by default as-or-more-native than anything Qt or GTK produce.
Without massive engineering work, handcrafting your GUI in Godot is going to suck for anyone using a screen reader, anyone who reads Arabic, anyone who can't use a mouse, etc.