Checked them out myself and yes, Gilliam's VF-25F didn't have the paint on the head. However, in some of the later episodes (4, 7 and 9) they also show Alto's Vf-25 without the paint on the head. I've a feeling they meant for Gilliam's not to have the paint, but ended up using the model with Gilliam's white head paint scheme in some scenes for Alto. It's weird though, the whitehead usually pops up in scenes where the VF-25 is coming up the elevator, yet they have a similar shot of the plane, with head paint in the intro.
Another thing, it also seems to indicate that they use separate models when animating the different modes which they then edit together to make it seem like a single plane transforming.
EDIT:
Just realized that this discussion probably belongs in this thread.