What about:
config interface 'wan'
option ifname 'eth0.6'
option proto 'none'
option auto '1'
No other options (maybe try MTU 1508 here and remove the config device section)
config interface 'pppoe'
option ifname 'wan'
option mtu '1500'
option proto 'pppoe'
....
All your other pppoe options
config device 'wan_dev'
option ifname 'eth0.6'
option mtu '1508'
No other options
If that also doesn't work. I don't know. Someone else maybe has better knowledge.
Last thing I would try is to modify the pppoe connection setup script.
(To override/change pppd mtu/mru paramters)