Seems like some internal genkernel logic changed since I used this feature some time ago. So with the latest genkernel-2.4.8 I had to change the kernel arguments gnap_overlay is using by setting an empty cdroot and setting real_root instead of the old cdroot. Just change one line in gnap_overlay, like this:
"s:cdroot:cdroot=/dev/${TARGETROOT} ${CACHE}${SERIAL}:" \
to
"s:cdroot:cdroot real_root=/dev/${TARGETROOT} ${CACHE}${SERIAL}:" \
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