Hi JustaOnegirl,
Thank you for sharing your thoughts about this side game! You raised a lot of good points and insights that I wanted to respond to so I will preface that this will also have spoilers!
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Yes there is darkness and bitterness in this version of events that isn't in the main game. This is a 'cursed' timeline. The reason why Deita feels so guilty during the whole game is because she knows it would've been better for everyone if she had "let the MC go" and get taken to the dungeons in the beginning but she couldn't help herself from wanting to spend more time with the MC regardless.
As you pointed out, the reason why the "gods" brought the MC to this world was to develop their creation. In this case with the addition of 'free will' to determine if and how much freedom to give the people in order to maximize their happiness without recreating the mistakes of the past.
What separates the Villain's side from the main game is that the Villains all use the Transient's One's potential freedom to ultimately double down on their most defining traits/desires. Jeth- irreverence/ambition, mikaylis- protectiveness/insecurity, deita- insight/dodginess. Verses in the main game the companions utilize the 'freedom' to develop and grow in a new way.
Therefore the gods may be less opposed to the Transient One staying in the world if their creations are developing in a positive way. The bitter endings of this game are not intended/planned to be directly mirrored in the main game.