Don't apply the body of the square to the edge of the timber, align it with the snapped line, the body running the length of the timber with the snapped line. Draw the mortice line along the tongue, perpendicular to the snapped line.
Not sure I read the question right or interpreted it correct.
Are you snapping two parallel lines on the same face?
I would have the brace stock re sawn to make it all more uniform. One possibility. Or scribe it. Or use square rule to reduce the waste side/inside to the ideal tenon. So, size all your tenons to 3" using 1-1/2" shoulder and 1-1/2" tenon/mortice. Make all your mortices the size of the largest know width stock, 6" and all the smaller ones will fit for sure as well as the big.
