About the only 'mistransformation' i've done is with my CHUG BattleTrap. In combined robot mode the rotor on his back sits flush and rigid with his torso which doesn't make for very dynamic posing. I found online a 'fan mode' to still have the rotor 'backpack' plugged in so it can be free-spinning and still looks good and he has his full range of motion now.

I have yet to try moving the wings on my God Ginrai combined mode to a lower height because its so damn fiddly to do, but now that Super Ginrai and Godbomber are separated for a while I may try next time I combine them again.