It doesn't matter if the vlan is end- to-end or local. What is important is for the subnet which the AP/WLAN will reside to be routable and being able to reach the controller and external dhcp server, if used.
You should understand that for the 5508 controller, the management interface acts as both management and AP manager interface. The management interface can be tagged or untagged, in which case the switch trunk port has to be untagged or tagged. For example, if you specify a vlan ID on the management interface, then the switch port must not have a native vlan ID.
If don't want the management interface to handle client traffice, then you can create another dynamic interface with Vlan tagging and map the WLAN to the new dynamic interface instead of the management interface. The Vlan ID on the dynamic interface must match the vlan created on the L3 switch. If there is a L2 switch before the L3 switch, then you just create the same vlan on the L2 switch but with no IP address as the routed vlan will be on the L3 switch.
Please refer to this link for better understanding:
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