Even if you have separated concerns by having method 1 return Monad transformer A and method 2 return transformer B, you will still have to combine the results of both your methods at some point.
Sure. But if you're doing it right, that combination happens in a place whose sole responsibility is doing that combination. The only case where you have to carefully interleave A and B is if your business logic really does involve carefully interleaving two disparate effects, and in that case the complexity is genuinely there in the domain and it's good to surface it explicitly (or else you're modelling it wrong).