I'm having the same issue as in the OP. Normally I set color order on the controller, but in this case, the flex strips I have are two different color orders, and they need to occupy the same output block on my 682 controller, so I need to set color order within xlights for one of these strings.
When creating a whole house model using the strings, the default string (RGB) color order one works, while the string using the modified color order (RBG) does not work correctly. It's almost as if in creation of the whole house model, the color order of the model was ignored. Not sure if this is a limitation of the whole house model?