Hello Adam
The truth is that sometimes Cisco does indeed do a terrible job at their descriptions. Let me try to clarify:
VLANs allowed on trunk - this shows the actual configuration that has been applied as far as allowed VLANs go. Whatever appears in the switchport trunk allowed vlan add command will appear here. By default, if you don’t issue this command, the default is 1-4094.
VLANS allowed and active in management domain - This lists those VLANs that are allowed on the trunk AND are currently active. What does it mean to be active? It simply means that the VLAN itself has been created. In other words, that VLAN must be listed in the output of the show vlan command.
I actually labbed this up and confirmed this. Essentially, this output seems to be a more legacy way of saying that the VLAN is created. It exists within the “management domain” of the VLAN database within the switch. The management domain doesn’t have to do with VTP or with the management VLAN, or management protocols.
I hope this has been helpful!
Laz