Many years ago (before eCS was ever thought of), I played with moving a few things around. The idea, at the time, was to reduce the amount of disk space that was required for multiple boot systems, by sharing some common code. I remember that I was able to move the network stuff to a common disk, and it worked okay, but it became a PITA when it came time to update. I don't think I tried much more, because it was such a problem to try to manage it.
Moving directories to other directories (IBMGS* to the \OS2\SYSTEM directory, for example), really doesn't accomplish anything, even if it does work, so why bother?
In eCS, there is now an option to move the PROGRAMS directory off of the boot drive. I highly recommend doing that (it should never have been placed on the boot drive in the first place). There is also an option, in the WarpIn installer, to put the default directories (TOOLS, and PROGRAMS) onto a different drive, and I have not, yet, seen a problem with using the same directories on multiple boot systems. I have also moved eCUPS to a common drive, with no trouble.
My main objective was to remove stuff from the boot drive, that really doesn't belong there (ie, it is not actually part of OS/2). The exercise is not complete. There are still things on the boot drive, that really shouldn't be there, but the arcihitecture of the system limits what can be done, and most of what is left is not much of a problem. The main advantage is that installing a new version of eCS, is very much simplified. The main disadvantage, is that I need to remember to do WarpIn installs from both boot systems, to keep the WarpIn databases up to date.