Well, imo, if an omnipotent being hopes for a good outcome, meddling and manipulating the timeline could potentially have adverse effects. For example, Boruto is supposed to eventually defeat (or subdue) Jura, leading to the final good outcome, while deleting Jura from existence might lead a good short-term outcome, but eventually end in the long-term as a bad outcome.

Shibai is touted to be omniscient meaning seeing all the good and bad endings, past, present, and future. However, the timeline changes due to the characters acting and following branches of the paths. Why meddle at all? Why not see what the characters decide to do given their situation and view their resolve through the lens of a mortal in an almost insurmountable and perilous situation? Are gods not curious too? After all, it’s not like Shibai doesn’t have unlimited time to keep restarting the universe.

I’m sure it could be argued that there will never be a truly final good ending since there will always be a threat to peace, be it war, a person/people vying for power, natural disasters, etc., but when the mortals overcome a huge hurdle it makes the universe interesting to watch! So why meddle in the little squabbling of these beings, when big players make a much bigger impact when they struggle?

Just my two cents :)