Several things going on here. The first is that the IPQ401x has, well, a unique way of dealing with VLANs and its switch and Ethernet phys.
There are various commits to remove the "hard-wired", internal VLAN tags. It's on my list to look at after I wrap some other work.
The internal, UCI-based switch config is, in general, a little challenging at times. Conceptually, the VLAN in UCI is a "table entry" that happens to default the tag to the same number. If you're using more than your switch's driver has for entries, you need to add the vid tag (and pvid) as well. Until I or someone else works out the locked-down, internal tagging, this would be "future".