I'm not sure I understand what you're asking. It seems like you're asking why your clangd extension isn't working? But then you say:

BTW I'm not talking about using clangd with the vscode flatpak package

If you're on Linux chances are using a package manager. Do you think the package maintainers won't compile the features(well maybe, Debian)? It still makes no sense as most users would have the feature anyway.