I'm not sure how libreboot handles UltraBay batteries but according to this wiki the regular BIOS actually first depletes the UltraBay battery before using the normal battery. You might find the settings you are after in the wiki as well.

thinkwiki.org/wiki/How_to_use_UltraBay_batteries

Maybe this bug is relevant too?

notabug.org/libreboot/libreboot/issues/56

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