Do you mean for the initial set up, or in general?
If the former, it's possible, but finicky in some cases. There's an issue here, and it sounds like it's in the works:
If the latter, I think it's a matter of the scope of the package. usethis is intended to set up and structure workflows — it's not a full-blown git client (à la git2r or the newer gert package).
You could file a feature request if you feel like there's a compelling case for it.