Consider a ship like White Base versus the SDF-1 Macross. Both are unique in their make and purpose but in different ways. The White Base is meant to do exactly what it does for the first half of its series - slip through enemy territory mostly unnoticed and repel assault with a minimum contingent of troops. It's meant to be a high-speed, small (for command craft), specialized ship.
The SDF-1, on the other hand, is a colony ship that's supposed to ALSO be able to defend itself from massive enemy assault. For this purpose, it needs space - lots and lots of space. What is the single most notable characteristic of a Super Robot?
IT'S HONKIN' BIG.
I think Osle's purpose with single-class ship captain was to cover more "realistic" starships while the multiclass covered the more fantastic ones (such as, I suppose, Galaxy Express 999. Yes, I know it's a train).
Personally, I picked a multiclass of Arcane and Super Pilot less because of specific features and more because I figured Hugo's mech needed a bit of "oomph", visually speaking (Cybuster has always been less-than-impressive visually for me). But I can't really think of a good example of an arcane/super mix.