I don't think VLAN is the hardware's problem. The FEC just sends whatever "data" you want to send after the MAC addresses. If you want a VLAN header then you have to add it (and parse it inbound). Here's what the frames look like:
IEEE 802.1Q - Wikipedia, the free encyclopedia
You'll notice that VLAN-Tagges packets are longer than the "legal maximum" for Ethernet. Is this an issue?
Section "19.1.3 Features" of the MCF5274 Manual states:
Programmable max frame length supports IEEE 802.1 VLAN tags and priority
So that should be fine.
If you search for "VLAN" in this forum you'll find the following post, which says that the uTasker TCP/IP stack supports VLAN:
Re: Which HTTPd is better for M5225X?
Tom