"We have a few custom packages at work which we would like to test with Knoppix to see how well they'll work before we go through the effort of remastering."

Really, the easiest way would to install Knoppix (or Slax) to the hard drive and see if your packages were compatible. There is a slight chance something still wouldn't work when the result was actually remastered--but the same would be the case with an arrangement where the OS was running from CD but the application running from the hard drive, as the most likely issue would be that something needed to be writeable.

The nice thing about Slax for this kind of thing is that it's set up to fit on a mini-CD, so it can grow a lot and still fit on a standard one. Knoppix may require a lot of included packages be removed before the remaster would work.

I have personally had better luck with remastering Knoppix, but Slax and Morphix (and maybe a few others) have the ability to add packages in a kind of modular fashion--included on the remastered CD, but not really part of the base .iso.