Here's what I think:
Equally trained Hork-Bajir Male vs. Equally trained Andalite male... the Andalite. Assuming that each one is about average in strength/reach. Keep in mind that Andalites may have better training.
Untrained Andalite male vs. trained Hork-Bajir male... Hork-Bajir.
Female Andalite vs. female Hork-Bajir... the female Hork-Bajir. Female Andalites have a much smaller tail blade, whereas female Hork-Bajir are less different than the males, although the males have an extra horn, and presumably larger size.
Another possibility is that, if the fight doesn't end soon, the Hork-Bajir may recover really quickly and be able to keep fighting; it took only seconds for Jara Hamee to heal that wound he made in his brain which was deep enough to expose his brain, and he recovered very quickly. There was no mention of an Andalite being able to do that, and no reason to assume that they can.