The biggest problem with putting a "thumb on the scale" to benefit one player over another is that it interferes with both players' natural development of an understanding of eco balance. The stronger player is going to have to fight against his own brain to make sense of a sluggish balance and the weaker player is going to be denied the opportunity to develop that aspect of their game sense. Which means neither player is going to get better. It will be not only a frustrating experience but also a pointless one.
It would make more sense to have a handicap in the form of one player starting with prebuilt structures. From there, the game would be completely normal: every unit and building would behave exactly as normal.
It's true that the stronger player could catch up to the weaker player and then the game would basically be over--but that just means the weaker player needs to learn how to play from an advantage. This wouldn't be for TMM of course, it would just be for custom matchups. It wouldn't just be about balancing 1v1s or 2v2s. You could balance a 2v1 this way, or you could balance a 6v6 if the weakest players got to start with an extra factory and some pgens. You would just have to expect them to behave as gentlemen and not give their factories to a higher-rated teammate.
You might be able to modify the "prebuilt bases" code to look at player ratings in order to decide how much each person gets of the prebuilt stuff. So if you this SIM mod running (let's call it "Balanced Bases") and prebuilt buildings are off, nothing happens. But if prebuilt buildings are on, the stronger players get less and the weaker players get more.