Yeah, I've run into this issue with Flatpak & Kate. (I think it was specifically the Flathub Kate Flatpak that was pulled?)
FWIW I was recently able to get a "passable" but not ideal Rust/LSP/Rust-Analyzer/Cargo setup mostly functional via use of the kate build plugin and e.g `flatpak-spawn --host cargo build`...
...and... `flatpak-spawn --host cargo run | sed --unbuffered 's/\x1b\[[0-9;]*m//g'`.
Excuse the cough. :D (It was necessary to remove the ANSI colour codes produced by some logging library the project used.)
(My preference would be to use AppImage but unfortunately recent Kate AppImage versions have a hang-on exit bug.)
I'm having the same issue with the Visual Studio Code (Flatpak). I want to use the compilers, interpreters and tools from the host, not whatever it's provided by the Flatpak or the runtimes from flathub/gnome, if it's provided at all.
A Flatpak may have to ship with an independent copy of a lot of basic developer tools, and even then I don't know whether I want two different versions of git access the same local repository with a chance of incompatible repository formats.