Flatpak can do CLI apps it's just mildly unwieldy because of the whole flatpak run ...
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If you want reproducible dev environments, yeah you're pushed to container solutions be it distrobox, Podman or Docker. Or something like nix as a user.
If you install a Debian distrobox it'll be as reliable as Debian itself is. It's only an issue when you're after 100% reproducible systems, which Docker can help somewhat with, or again, nix. Or NixOS if you really want it all system-wide.