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Then you have to introduce another system (SABRE) and integrate it with your system instead of just using the same Raptor engines being used in the second stage vehicle.

One benefit of Raptor is that its designed to be mass produced. Achieving cost efficiencies with scale.

Adding another engine means, one more production line each with less production volume (i.e. less efficiency of scale).

Air breathing engines don't work well with the flight profile of vertical launch systems. Sabre wont develop near enough thrust to get a Super Heavy + Starship stack off the ground.