Not sure about injecting jcms with the erc after loading the figure or clothing as the erc may be getting linked (ie the slave dial linked to its controlling joint) on load of the figure and injecting it after might no longer work as an erc, but only as a dumb dial like other morph dials. Do a simple erc of any morph (even one that just moves one vert) to test it out before you go too far :) 

I'm not sure I understand why you want to do this as I haven't followed your development so I can't suggest any alternatives, but goodluck! :)

As for alternative geometry to give alternative mat zones... aside from carrying extra materials in the figure section... each bodypart in a cr2 can have its own materials that do not have to be read from the figure section.  Look for the "customMaterial 0" line, turn this to 1 and then have your material channels under there.  This is how partial bodypart mats were treated at least since  Poser 4 (may have started way before, but this is when I saw them for the first time.) These have fallen out of use since people just over-ride the materials in the figure section only. One thing for you to check:  once you declare customMaterial for a bodypart I'm not sure you can remove it again to make the bodypart go back and obey the figure materials  without reloading the whole figure from scratch. 

You'd have to test this in all the poser versions you plan to support, maybe even other apps like ds. Not really the fun part lol 

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a sweet disorder in the dress kindles in clothes a wantoness,
do more bewitch me than when art is too precise in every part