Hi there,
I am surprised to find that Genie projects tinker with project.toml in a way which makes it incompatible with version control. Hence I regard this a bug.
Concretely the field instantiated_pwd is set, I think by GenieBuilder, but I am not sure, to an absolute path of the current directory, which usually will include the user's home.
As the field seems unnecessary, I would suggest to simply delete it.