It's indeed an inconvenience with developing with Flatpak, but assuming someone still wants to do it, here's what one can do to make it practical (as far as it can be):
Get your development tools as a flatpak runtime extensions
Try to do everything inside the flatpak'ed tool (so e.g. with VSCode, use the terminal built in it, rather than a separate one)
If you need some tooling from the host, you can bind-mount them in. Just note that they probably have to be somewhere outside /usr because that's where Flatpak mounts its usual runtime