Do you understand that is a just to test waters at first right?
Towers himself is using this negotiation to see how Eggman is willing to compromise. He hate it but he very much understand getting Eggman's help would be a boom.
Prove we would keep our word they probably be willing to extend the truce until we be ready to storm the Ark and consequently the Black Comet. Towers said himself, Black Doom is threat to everybody, open a second action, while nice, is not much of a game changer as you believe.
You are really underestimating how difficult is to truly fight Black Doom and how easy is his winning condition. He needs to get the Seven Chaos Emeralds, that's it and he won. He would activate the Eclipse Cannon and wipe out everybody that could be a threat.
The fact GUN and the Restoration are even willing to talk with Eggman and the doctor is considering to even speak with them, despite being mortal enemies, speaks volumes of the threat they represent.