The reason I ask is because these instructions seem to indicate that setting up a slave is different when using xtrabackup.
Yes, it certainly is different. MySQL has a LOAD DATA FROM MASTER command. It's deprecated, locks all tables while it's running and it only works on MyISAM and ARCHIVE tables. It doesn't even exist in MySQL 5.5.
If by "mysql native master/slave replication setup" you were referring to mysqldump, mysqlhotcopy or a filesystem copy while the master is not running, these all require the same locking (or shutting down) of the server as LOAD DATA FROM MASTER and mysqlhotcopy will only work on MyISAM and ARCHIVE tables.
XtraBackup, on the other hand, will copy all your InnoDB tables from the running master without locking any tables and will only lock the MyISAM tables at the end for the minimum time possible while it copies your MyISAM tables over to the slave.
While the process is different, the end result once you have loaded the backup into the slave is exactly the same.