After burning a lot of time on this issue, I found out that with the stock firmware, vlans will probably work, as long as you don’t use id=1 or id=2.
Unfortunately my ISP requires vlan id=2.
From what I can tell, this limitation is partly due to the qualcomm chip, but mostly due to a poorly thought out linux driver.
So I flashed OpenWRT (snapshot version), where a workaround is possible. For instructions, see my post to the OpenWRT forum thread here: IPQ40xx Switch Config "Strangeness" - #66 by rvl - For Developers - OpenWrt Forum