Why did the Tar-Aiym, if they were able to build a weapons platform capable of affecting other galaxies, feel the need to develop and unleash an uncontrollable plague? Earlier exposition makes it sound like some kind of Resident Evil style lab accident, but seriously, the weapons platform from Flinx Transcendent could have wiped out the Hur'rikku in one or two shots!
The Tar-Aiym were ambitious conquerors in their own right. Possibly they'd wanted to avoid destroying the Hur'rikku-occupied planets altogether, having had designs on that region of space for themselves. By the time they realized the plague had jumped species and was wiping out more than just its target race, it was already too late to burn the border zone's planets as a quarantine measure.
The thranx were fighting the AAnn for generations before they encountered their first humans. Given that they already knew of one vertebrate race that had achieved interstellar travel, their level of astonishment about humans' having done the same seems a bit overstated: would hair vs. scales really seem like a significant difference, in light of all the other similarities between human and AAnn physiology? If someone's already met a talking ant, a talking beetle shouldn't cause as much of a shock, even though ants and beetles differ in many respects.
The events of The End of the Matter are the universe throwing a practice run at Flinx, saving three planets from a black hole using a designed key, a warm-up to saving the universe from the Great Evil using himself, a similarly designed element.