Just an idea... maybe instead of/in addition to releasing a full kitchen every time a "delta" is released, which is just the changed files/folders. There are several apps out there that can do that, and that makes for a more efficient download for people who already downloaded the kitchen once.
That way you could modify the option.xml files for the OEMs you want to be selected/deselected, and all or most of those would be preserved when you applied the latest kitchen changes (since most OEMs are the same from release-to-release).
Probably not the solution you were looking for, but I think without the source code to the buildrom application, there's not much we can do to change the way it functions.
Also, here's my super secret method--I set all of the option.xmls to be enabled by default, and I just move out the OEMs I never use outside of the OEM directory. That gives me my core list--as I find another OEM I want to add/mess around with I just add it to the OEM folder. Again, it sort of defeats the process of the checkboxes but it's quicker for a non-n00b like me.
