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