I wanted to use IntelliJ (Flatpak) with Rust tools installed in a toolbox, which I think is similar to what you’re doing here. The bridging between these different containerized environments is pretty clumbsy imho. The expectation is that IntelliJ shouldn’t be calling rust binaries directly, but instead wrap them with flatpak-spawn.
In my case that wasn’t possible due to the way the IntelliJ Rust plugin expects to be configured. It wants to be pointed at a folder instead. See my post about this for details.
Anyways, I ended up installing rust the manual way into my home folder with rustup and not using a toolbox.