flatpak config is missing "command" property
and that means it fails to work from Builder.
Just add:
"command": "gnome-characters"
to the manifest.
I went to push a fix for this, but it looks like master is a protected branch. Tangentially, that sort of goes against they way we've worked in GNOME for a couple of decades and something that should be carefully considered if it wasn't already.
Edited by Christian Hergert