Sorry to take so long to answer this post. Life has been busy recently!
Unfortunately, MakeOTF (and the underlying libraries shared with FontLab) always set the CFF encoding to StdEncoding, and there is no way around this. We do expect the bug in Illustrator to be fixed in the next release.
The only way around this problem that I know of is to use Just VonRossum's TTX tool to dump the CFF table as XML, edit it, and then recompile it back again.
I suspect that you could also make the font as a Type 1 font with the desired encoding, use the CFFChecker tool in the FDK to convert it to a CFF font file, and then use OTFTableEditor to copy the CFF file into the target OpenType/CFF font. You will need to check that the glyph order is the same before and after, but this should be the case.