This problem was bugging me too, I found your post and was disapointed there were no solution.
So finally I did some investigation and build my own solution. The idea is to wrap bc2 exec. The wrapper just check if the content of the file is zip or not, if it is, it rename the tmp to zip and then run beyond compare.
I did that in java, maybe it could be done faster with some other language but anyway. So you need to compile the attached src, package in a zip and then wrap it in a exe (with launch4j for instance). Or you can directly the exe

C:\Program Files\Beyond Compare 2\bcmks.exe "{3}" "{4}" "bc2"
Regards,
Matthieu
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