I prefer the idea of having the piloting skill be for your primary ride. If in any other chassis type, you get -1 to the skill. Or the skill is the baseline, and you get a +1 when in the primary ride. Either works. So it wouldn't matter what version of the Hunchback you were in, you'd pilot them all the same. But move into an Enforcer or Thunderbolt, and you'd be a lesser pilot for a while. How fast the new ride becomes the primary is up in the air - I use "as needed for the plot", but I'd agree that the better your skill, the faster the new one is learned. I wouldn't have a problem with there being an additional -1 if switching between quad and humanoid, but could be talked out of it.
I also like having separate skill rolls for piloting and jumping. If I've been a Hunchback pilot for 30 years and then get re-assigned to an Enforcer, I would expect to suck at jumping for some time. I've had characters that were an average pilot when running, but that were either very good, or very bad, at jumping. It doesn't matter so much whether jumping is a separate skill, or merely a modifier to a skill, as long as it is listed for every character.