Hello Narad
Yes, that is correct. Protocols such as VTP, CDP PagP, and STP will always use VLAN 1 even if VLAN1 is not allowed, and even if VLAN 1 is not the native VLAN. Such frames will always be processed by switches on VLAN 1. The only exception is DTP, which always uses the native VLAN. So DTP may not function correctly if there is a native VLAN mismatch.
I hope this has been helpful!
Laz