So there are two differences to point out here. Management VLAN does not necessarily equate to native vlan. The native vlan is simply the particular vlan that is not tagged crossing a trunk port. This native vlan needs to be the same on each end of that particular trunk and that is it. So a trunk between switch A and switch B the native vlan could be 6 and on a trunk between switch A and switch C it could be 42.
The management vlan is typically the vlan we put the layer 3 ip addresses of our network equipment into for managing the boxes. So if we choose to make the management vlan 100 for all of our equipment we will make sure that vlan 100 is trunked to all of our equipment, but it does not have to be the native vlan. Then we will set the layer 3 interface on our switches to be in vlan 100 and give it an ip address on vlan 100.
Hope that makes sense.