I think those armadas are there to demonstrate that the core factions are still much bigger and much older than the player faction. They were added, I believe, in response to players thinking the core world factions were pushovers on account of having nothing but a few small patrols and stations defending their holdings. Chicomoztoc has two orders of magnitude more people than the player faction, and a military tradition dating back centuries. Even now, the other factions' defenses are much, much lighter than they would 'canonically' be.
That said, it's not as if the player faction doesn't have a unique S-modded fleet defending its interests.