Like I notice in Codex in PhpStorm it uses Get-Whatever style PowerShell commands but firstly, I have a perfectly working Git-Bash installed that's like 98% compatible with Linux and Mac. Could it not use that instead of being retrained on Windows-centric commands?
But better yet, probably 95% of the commands it actually needs to run are like cat and ripgrep. Can't you just bundle the top 20 commands, make them OS-agnostic and train on that?
The last tiny bit of the puzzle I would think is the stuff that actually is OS-specific, but I don't know what that would be. Maybe some differences in file systems, sandboxing, networking.