First off thanks for the newish Tier 6 material and this newest addition, the 'upgrade' material. It's not that bad on many ships.
But, I've noticed on the Mat'ha raptor, choosing the 'Upgrade' material completely disables any hull pattern choices (coloring etc.).
See here:
http://postimg.org/image/6r4tyypgv/
You can clearly see the 'pattern' boxes aren't present at all, unlike with other hull materials (like here:
http://postimg.org/image/zdeyn9oxv/).
I've also checked that other T5-U and Tier 6 ships do get an option of hull patterns even with the new 'Upgrade' material, including the Mogh.