Seems appropriate that my first contribution to this thread was a Belle-centric omake then, because the question of how 'benevolent' Eggman can be while pursuing his goals is basically the question that Belle asks of Eggman.
He wants, demands control. Thematically, this is why he's robots and industrialization to Sonic's freedom and nature. Putting him in VV lets him develop and be the 'lesser evil,' sure, but he's still not a good guy by any means at this point in time. He's got bigger fish to fry and has a scarcity of resources, so he's forced to divert from his typical MO. But he still wants to do all that.
Can he develop kindness? If control really is necessary and Eggman is going to be the lesser evil in this messed up world, can he make good come of it? Or will he only be the lesser evil for as long as he's not capable of being the greater threat or it's not a conflict of evil vs. oblivion (such as with the Black Arms)?
What enhances this, since people brought up Eggman's forming squad of kids, is that all of them are inherently loyal to him or his ambition. Except for Belle. Cubot and Orbot, bumbling sidekicks, but loyal. Sage, she grows emotionally throughout Frontiers, but is not going to defy Eggman. Metal's literally got his free will shackled to not overthrow Eggman and otherwise tries to accomplish the same overall goal, just with himself in charge instead because he thought he could do better and wanted to surpass Sonic.
Belle is the only one without a trait that keeps her loyal. She has the potential to flat out leave Eggman if she decides that he's too evil and has nothing left of Mr. Tinker in him, in addition to the fact that losing Canaan would have meant losing her.