Keeping things out of the gutter for a moment...

From a toy POV, Ultra Magnus is very much like a Mega Pretender (i.e. both the inner robot and outer robot can transform; although Mega Pretenders can combine in vehicle mode; I'm not sure if Minimus can combine w/ the Magnus Armour in vehicle mode (or if he just rides in the trailer)). From a canonical POV, Ultra Magnus is something entirely different from Pretenders. He is a load bearer, which means that unique features of Minimus' Spark allows his body to specially augmented like a Russian nesting doll, carrying one or more "loads" at a time. In the IDW comics, Minimus carries two loads - a larger Minimus Ambus shell, and the Magnus Armour. This toy carries a single load; the Magnus Armour.

This is also a homage to the original G1 Ultra Magnus toy who, as we all know, is a the same body type as Optimus Prime, but the trailer transforms into power armour for the cab robot. Now of course, Alpha Trion was never anything like this, but as explained, this decision was most likely done to make the Minimus toy more appealing to the general Japanese market, most of whom would have no knowledge of Minimus Ambus. I personally prefer the Hasbro version, as Minimus Ambus makes way more sense than Alpha Trion, but I can understand why TakaraTOMY made that decision for their market.

At the end of the day, if a few colours here or there really bother you... repaint it yourself?