Is it possible for the master (5.1) to have innodb_file_per_table = 0 and for the slave (5.1 or 5.5) to have innodb_file_per_table = 1 ?
Yes you can use
innodb_file_per_table = 1 for your slaves.
Additionally take below points in your consideration
If you have same version on MySQL on both Master and Slave. You can directly take backup and setup replication from Master to Slave by adding
innodb_file_per_table = 1on slave in
Please have a look at How to set Master Slave replication
If you have different version of MySQL , Please make sure that you are taking backup properly because different version would have mismatches in System tables (MySQL Database).
Please have a look answer by
@RolandoMySQLDBAfor How to take backup properly