If you're a Bastion, you can freeze Thresher Maws with Stasis, and bullets can still hurt them. Easy pickings
What they show us is that the galaxy is at peace. The large-scale indoctrination you seem to want would render that outcome impossible. At best, indoctrination leaves organics as mindless husks incapable of higher thought, and at worse it makes them actively psychotic and violent, as we saw with the Salarians on Virmire or Rana Thanoptis.
So yes, barring a retcon I have plenty to go on. What indoctrination may persist clearly was not enough to derail galactic recovery or progress, and therefore can be dismissed.