Why should I prioritize top tube length over stand over height on a CX bike?
Why should you prioritize top tube length over stand over?
Because top tube length affects fit and stand over does not affect fit.
When you are riding the bike stand over does not affect fit.   

My CX only has 1" of stand over.
A big triangle is good for stiffness and shoulder carry.
A tall top tube means faster transition to shoulder carry.  

I don't get your reasons  


1" versus 4" should not affect your ability to dismount quickly.
You ride on the seat - not the top tube.
In a controlled dismount the bike is stopped - 1" is a quick and safe stand over dismount.
If you have to bail because a truck pulled in front of you then lay the bike down - don't stand up.
So your clothes touch the tube?  What is the harm?
How is more clearance better on uneven ground?
When you stop then don't stop over a hole.
If you fall on the top tube an extra inch of clearance is not going to save you as your feet are not going to be under and you are going to be moving.
Even with 2" of clearance falling on the top tube should always be your last choice.