I'm bringing this up because I haven't seen anyone fight dark bosses in speedruns and I feel like they could be worth over fighting ukumari/runapuma because they are really long fights and the dark bosses are much shorter. are they not allowed or is everyone just like scared to fight them?

It is allowed, I'm not sure about other characters I haven't tested it much but for rumi it takes up too much mana if you want to clear it quickly which would not be good after clearing ukumari or runapuma. Just for reference, as rumi it takes about 1min30s to clear runapuma and about 1min40s to clear ukumari. But it might be quicker if you use other characters like qaru or nayra with powerful ults and have stronger melee attacks than rumi.