It’s really difficult to believe that Chrysalis spent more than a millennia leading a species that has this incredibly convenient evolution that could’ve been triggered by any rogue drone just happening to have a change of heart. Since the events in Fiendship #5 are told from her perspective while in captivity, I feel there’s three different options to explain it:
Comic discontinuity: She entirely fabricated her origin story to hide the reality that her hive has only been around for a short time, hasn’t done anything worthwhile in all of it’s existence and is being kept in a sub-optimal state due to her desperate need for control.
Comic continuity: All of her backstory is accurate, she used to lead a larger empire that somehow didn’t achieve this all-positive evolution for some reason, but after being magically blasted by Celestia was forced into hiding for possibly up to a millennia. Just like pretty much every single villain or major event in the history of Equestria, she happened to be pulled out of her torpor and became relevant again in response to the events of the show.
Middle-ground: Most of her backstory is accurate, but she’s purposefully leaving out that Celestia’s magical blast, the one that was strong enough to blow holes into her went even further and is directly responsible for turning future generations of drones into mutants whenever they trigger that deeply ingrained magic within their DNA through friendship. From there, it can be assumed that Chrysalis either couldn’t achieve the same result and culled entire hives whenever it happened or that she realized mutation would make her sterile and just left them to die off on their own before starting over. Given how her strategy after the events of S6 shifts to ignoring the mutated hive and being by herself, I’d be inclined to go with the latter. It would ultimately explain why she hasn’t been able to reliably expand for all this time, has this need to keep her hive starved and yet hasn’t been overthrown by a rogue mutant hive or mutated herself.
It’s pretty clear which one is my favorite, but the others are just a valid TBH, if not disappointingly so.