Documentation says "Native replication is the default, unless other operation is specifically configured." ( http://doc.powerdns.com/html/replication.html )
By Native it is referring to a replication thats native to the backend you use where it does not need to take an active part in the process itself but just uses the data it is presented with. For most people MySQL Native thus usually means MySQL Replication although a combination of rsync and mysqldump technically could also be called that.
PowerDNS Server does not support incremental zone transfers (IXFR) but does employ AXFR. For really big zones that would mean increased network traffic between your nameservers. Also i don't have any experience with what happens when the Zone is bigger than available RAM. PowerDNS Server might choke then.
A AXFR Master/Slave can be setup with only the BIND Zonefile backend i.e. in 'traditional' BIND8/9-style, however if you are planning on deploying DNSSEC with PowerDNS a dnssec-capable backend such as MySQL will be necessary for the metadata and key storage.
Most people going for a pure PowerDNS Server setup are using Native (with MySQL) Replication, so this is also the topic on which most support information from PowerDNS Server users is available.
With MySQL replication chances to all of your nameservers are near instant which provides a smoother user experience if you let clients change their own zones/records for example via some web frontend to the database PowerDNS Server uses.