I think you mean 0.6.1, yeah? Well unfortunately you'll still have issues with fastLED because it gets compiled first and is including application.h before PARTICLE_NO_ARDUINO_COMPATIBILITY 1 is defined, which will define RwReg, and fastLED then redefines RwReg.
I think for right now in your situation I would advise sticking with 0.6.0 firmware until we sort out a solution (I think as described in Future Thoughts above). You don't need PARTICLE_NO_ARDUINO_COMPATIBILITY with 0.6.0.
You can specify targetVersion: '0.6.0'
with the JS API https://github.com/spark/particle-api-js/blob/master/docs/api.md#compilecode