It was one of their own who understood it, so how does it follow that they couldn't? Knowledge of it is elusive (seemingly even across the stars Meteion encountered), but the only reason it is lost is due to Kairos and Venat keeping it all a secret. Even the sundered could not understand it until the events in Elpis help confirm some theories on the matter, i.e. knowledge derived from an ancient.
As to manipulating it, they could not easily do so by default, but they had 1) familiars they could devise to do so, like Meteion, if something similar was devised without the design flaws (and it's an open question whether a prayer-filled construct like a primal could do it, as Elidibus did seem to surge with power due to prayer when transformed into the WoL primal form) and 2) areas like Ktisis Hyperboreia, which had aetheric suppression fields that could potentially allow for the the power be honed. Amongst other workarounds they may have devised, given the chance. Hell, they could even sunder a few of their own, since it only took 8 or so to ultimately defeat Endsinger in spite of her swallowing several worlds' worth of despair... plenty of options, but since they were never given a chance due to the time travel mess being used to explain it all and act as a constraint, so Venat did not share any of it, and all that was never considered. Zodiark, even sundered, could act as a shield for at least the past 12k years, if not more, so they had the time to figure out a plan - many plans, even.
On Zodiark and how she presented him and his minions (a minion being someone carrying out the will of their master), she is referring to them as evil and she is referring to them as darkness. See e.g.
here, and
here she is referring to Zodiark as the darkness. It is not difficult to see that there is indeed an insinuation being formed here that he was evil - according to her phony recollection of events, anyway.