The expectation is that assignments in a multiconfig override the same assignments in the base local.conf. For example, a MACHINE = "qemux86-64" in a multiconfig/qemux86-64.conf should override a MACHINE = "qemux86" in local.conf. At the moment (poky a92d27acd8) it doesn't do that because cookerdata.py parses the multiconfigs first.
probably the same as https://bugzilla.yoctoproject.org/show_bug.cgi?id=10757
http://git.yoctoproject.org/cgit.cgi/poky/commit/?id=d8d2f421d673d9988d6db017d0e5c0e9e6b63396
Verified, in commit def638ebd69cef217ca567352bc08920b79ca03d this issue is not present.