The tenon centred in the mortice i.e. not skewed and with equal amounts taken off of both faces. Planning to fiddle with tenon faces to position your style/rail correctly seems a sure path to insanity.
I do strike all my gauge lines from a marked face or edge using dual pin mortice gauges. I have experimented with a Veritas disc type mortice gauge but find the ones with pins easier to use in most cases. I still have the Veritas but I find the pin variety (which can be bought for pennies at any car boot) a bit steadier in use as the stock rests against the fence and the beam of the tool rather than just the fence as with the disc type. Still, the disc one does cut very cleanly and has its place for certain tasks.
Thinking some more about sitting astride the stock as you mortice it; I assume something different is done when morticing the edges of styles in, for example, the edge of a style to be used in a cabinet door? Do you pack the stock out somehow and sit on it or just do those types of jobs on the bench?