Lincoln was not on the ballot in southern states because southern states refused to put him on. Why this should be considered Lincoln’s fault in some way or impact the legitimacy of his election, as you seem to imply, is beyond me.
Let us assume CRuz is nominated, and a number of blue states keep him off the ballot. Which I think they could do constitutionally, at least in theory.
If he nevertheless wins a majority of the Electoral College, is his election somehow less valid or legitimate?
Lincoln won an absolute najority in the College, an impeccably constitutional result. The southern states just didn’t like that result, so they took their ball and went home.