The recommendation regarding the native vlan might be important for some platforms (there was a thread about that just few days ago). On the 6500, it should not be necessary.
Keeping all the vlans allowed on the trunk (and avoiding instance 0, that what I see you are doing) are just suggestions for engineers who are so used to PVST+ that they could be surprised by MST behavior. Considering that you are planning to use a single instance, all this is not applicable to your case anyway. I would just use MST with absolutely no configuration (i.e. I would not even map all the vlans to instance 1), and everything should be fine with your third party bridge running a "real" (non-PVST) RSTP.
I'm working on a project that includes basic router configurations. I configurated everything including: line console 0, line vty 0 15 and secret passwords. There are 3 routers in the network and every LAN is going t...