Was this covered in the haka episode..?

I have myself a question and I want to make sure it wasn’t covered already: why is there a haka in the iron legacy timeline if there are only two hakas?

Because the merging of the various Haka’s into the two we know wasn’t instaneous.  We got told Eternal Haka from the Final Wasteland was part of the OblivAeon fight and got absorbed into the two Haka’s before it was over.  Overall, the explanation for Haka’s power source caused by La Comodora is essentially a massive Retcon.