SQL Server setting up logins for backup site
I was wondering whether I should transfer the NT Service,NT AUTHORITY and ###MS****### logins from one server to the other

No need to transfer those logins, because they are created automatically when you install new SQL Server instance
By the way, easiest way to transfer other logins from one server to another, is to use sp_help_revlogin procedure:
How to transfer logins and passwords between instances of SQL Server