So if you posted a video, it's not showing, so I'm not a hundred percent sure of the issue you are having. Also what version of Poser are you using? As Darryl said:
One of Poser 11's spiffy new features was for joints to automatically adjust to extreme morphs. Poser's had the ability to manually link joints to morphs in previous versions as well. Should be in the manual, or try asking at the official Poser forums.
But If I do understand what's happening, then yes, there are ways to fix the issues you are seeing by using dependancies and a combination of MCMs and JCMs (master control morphs, and joint control morphs) and it's just fine if the morph spans more than one body part when using either of those.
What I would maybe search for is a tutorial on making eye close morphs, because this is probably the most common place where people run into the sort of issue I think you are having.
All that being said, I'm not up on the newer features with joints in Poser 11, but I'm pretty sure prior to that the skeleton does stay the same size. I loaded up the Beast horse breed for Harry, which is huge compared to the normal size of the figure. There were a lot of JCMs built into that breed, I think to resolve just these issues. As an experiment I also loaded up a dynamic item for Harry I've been working on, sized it up to fit the Beast, and then put it through the fitting room to create a skeleton based on that skeleton of Harry with the Beast morph. When I took my new figure into the setup room it had the much smaller skeleton of Harry's regular size (which is what I expected, but it was the only way I could think of to check).
So any way, it is doable.