Yes you can and you can "split" an existing file by saving a copy and then using Manage | Database to edit the copies into front and back ends. The data end, however, doesn't usually need many, if any relationships. The only case where a relationship is needed in the data file is for calculation fields that refer to related tables and any scripts defined in the data end that need them to be performed correctly. (Once in a while, a "run with full access permissions" script must still be defined and perfomed in the data file instead of the interface file.)
1) Is there a downside to, initially, leaving all relationships in both files then cleaning them up during testing?
2) If I am using "auto-enter" from data in a related table, will I need relationships defined in the data file?
1) None that I know of.
2) If the auto-enter expression refers to values in a related table, then yes.