The rafter is typically placed to align with the bottom surface of the roof, so the way to control the seat cut is by drawing the roofs with the pivot line where it needs to be to show an appropriate seat cut. For a full seat cut, just draw the roofs using the inside face of the wall, rather than the exterior face. There won't be an actual cut in the rafter, but it will look okay in section view.
Another alternative is to use an object like MASTERAFTER_WD, available at ObjectsOnline, which gives you more control over the birdsmouth.
Richard
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Richard Morrison, Architect-Interior Designer
AC26 (since AC6.0), Win10