Yep, I know what you mean. The article is referring to tagging a native VLAN on a trunk port. When you're doing VLAN configurations on a host device (not a switch), the untagged VLAN on the host ("eth0" interface) implies the 802.1q "native VLAN" on the switch port.
int gi0/1
sw mode trunk
sw trunk allow vlan 1-50
sw trunk native vlan 20
Here, on a trunk port, VLAN 20 will be untagged as the frame exits the port. When the end host receives it, untagged, this is the "eth0" interface on the host. The Linux VLAN driver won't tag VLAN 1, however. In this particular switch port configuration, if you DID want VLAN 1 to work across the trunk port, it would then have to be tagged; Gaia (the VLAN driver) won't do this.
Likely not an issue for you. For you, your native (untagged) VLAN on your network is likely already VLAN 1 anyway.
Check it on your switch port (here's mine on one of my switches):
#show int gi0/8 sw
Name: Gi0/8
Switchport: Enabled
Administrative Mode: trunk
Operational Mode: trunk
Administrative Trunking Encapsulation: dot1q
Operational Trunking Encapsulation: dot1q
Negotiation of Trunking: Off
Access Mode VLAN: 20 (External_WAN)
Trunking Native Mode VLAN: 255 (Native)
...
Trunking VLANs Enabled: 10-12,20,254,255,901-903
On your 3200 gateway, your "eth0" (or "eth1", whatever) native interface is the IP for your network's "VLAN 1" subnet.
Configure all the other VLANs like you want (VLAN 10, VLAN 20) for your FlexConnect VLANs, configure the gateway's VLAN sub-interfaces (eth1.10, eth1.20), add those VLANs to the switch port VLAN trunk, and your FlexConnect AP trunk port.
"show span vlan X" to see if you got it right.
Caution: *PLEASE* use "switchport trunk allowed vlan x,y,z". Allow only the VLANs you require. Why? Just because your host doesn't have a VLAN for that network, doesn't mean the switch won't try to emit tagged frames for it! If you don't want VLAN 250 on that port, then don't allow it. Multicast frames gets the same treatment as Broadcast frames, and you can end up flooding your interfaces for traffic you didn't expect (#HasHappened; I got the t-shirt, and the emotional scar).
If you use "sw trunk allow vlan add X" then you can remove a VLAN with "sw trunk allow vlan remove X". Yes, "sw trunk allow vlan all" is a command but you're not gonna use that, right? 🙂