Interestingly, it's also the premise behind the Chthonic Horns from the Touring Anagnorisis quest, who experiment with 'natural' methods of growing and cross-breeding plant life to see what manner of results this could yield (but no, they'd never have the curiosity or ingenuity to deal with the true cause of the Final Days...) I do think the quest that fomented the notion that they were, on some level, a dystopia, was the Community Cohesion one (and again, the quest NPC for that is not called patronising in the FR localisation, but rather, charitable, which lends itself to what you say - even if at times they were a bit confused by your character, the way they behave is not driven by malice but good intentions.) I always took that quest as expanding on why they were able to achieve the sort of society they had, i.e. working on suppressing their worse instincts and focusing on channelling their power and individuality through intellectual (and I'd guess, artistic) means, which makes sense given the sort of beings they are and the powers with which they're naturally endowed.
The thing that is abundantly clear from all the lore we have built up for them is they differed as individuals, and these differences also manifest in their attitudes to their creations, as well as having their own virtues as well as some vices in certain cases. Even so, with the worst possible reading of their stance to their creations (which are beings quite far removed from what they are in many respects, even more than regular animals are from us), they still by and large tried to minimise their suffering and integrated them into their societal purpose (=better the star), i.e. everything had its place and purpose. In addition to some treating their creations affectionately, as we would a pet.
Even in terms of dynamism, be it the example you cited, or Themis's raring to go attitude in Pandaemonium, they were not wanting in that respect.
On a separate note, another thing they tend to get weirdly blamed for, i.e. just jumping to summoning Zodiark, also seems to have only come about after they tried other methods (although I thought that was at least implied anyway, but it's clearly stated here):
https://youtu.be/EBfCrns8-9I?t=148
I just hope Pandaemonium isn't another case of me questioning whether they even remember the characterisation of the ancients they built up in SHB, or even as recently, in EW via Elpis.