I don’t see this mentioned anywhere and I just want to be cautious - should I auto tune my quadplane? There’s significantly more flex because of the wings than on a copter, so I’m worried it might overstress the airframe.
Unfortunately, Autotune in ArduPlane is only available for the fixed-wing stage of a quadplane. Manual tuning of the VTOL stage is still necessary; you can find the necessary tuning parameters in the Q_A part of the full parameter tree. The default values are usually good starting values, but if you are concerned about vibrations and such you can start with lower P values and work your way up from there.
As you have mentioned, the flex is definitely a problem which will significantly affect the yaw, and I have observed this while tuning a styrofoam-based quadplane. So I suggest you improve the mechanical design of the wings (e.g. adding carbon-fibre rods that span the wing length, although this compromises on weight) to reduce the amount of flex before tuning.
Thanks, makes complete sense - I’ll tune old-school 
I did notice trouble the the frame stablising yaw - I’ve added some carbon (Skywalker X8) but the spans are so long it will be hard to fully stop flex.