Knee / Quill interaction?

I posted a Shoptask specific version of this question earlier,
but the core issues apply to many machines.

How does CNC deal with two axis that are parellel to each other,
like the quill and knee of a Bridgeport?

I know the simple answer is to only motorize one of them. But
there are pros and cons to each, and some benefits to controlling
both. For example, the quill weighs much less, is easier to
move, and is more accurate. But it has limited travel. On the
other hand, the knee has lots of travel, but is very heavy, and
on a worn machine may cause errors unless it is locked.

It seems that a good solution would be to motorize both. Use
the knee to adjust for large differences in tool length, like
an end mill in a collet vs. a long drill bit in a drill chuck.
Then lock the knee and use the quill for the actual machining.
(The same thing can be done with a manual knee - adjust the
knee manually when you do a tool change.)

The question is, how does the control deal with the changing
position of the knee?

John Kasunich