When staging an LFS tracked file, the file is staged as a regular file, rather than being processed by the LFS hooks to end up with a hash text file.
For the time being, I created a command "Add to staging" that runs git add on the selected file(s).
If the independence of git means bypassing the git configs, perhaps it is better to depend on installed git, maybe as a dependency for the install package... Anyway, just a thought.
Happy to provide more information if needed.