Apparently, tinting color values do not show up correctly with Robo-Goblin or similar morph abilities (Bear Form, Stone Form, didnt test the others, but I'd assume the same).
Basically, I had tried making an artillery unit that had to transform into an immobile version of itself in order to attack (basically Siege Mode). The mobile artillery was tinted blue, the immobile artillery green. Upon casting the morph ability on a newly created artillery, the artillery was correctly replaced with the other artillery, however it retained its blue color. When I morphed into the mobile version it turned green. From there is proceeded to alternate colors with each cast of the morph ability.
Also, while this probably known, if you fail to give the alternate unit the ability, you can move the alternate unit without it's model. (The model will stay in place and play animations regularly.)