Please let me be clear that the following is just an idea for a possible and versatile solution; it's not a feature request nor a bug report (I'll add separate posts in the Feature request forum).
I can see the problem of Bladerunner quite easily, and I think a solution could be as follows.
Once it is clear which partition to boot from (the user has selected a one, or from boot.plist), look for a sub-directory of Chameleon's Extra directory that has the name of the UUID of selected partition. If so, files in there such as boot.plist, DSDT.aml, smbios.plist, and also Extensions.mkext or Extensions subdirectory will OVERRIDE the item in Chameleon's Extra directory.
Thanks,
dp35dp