I'm pretty sure the power commander on its own does fuel kill. I don't have an ignition box but I think you are correct that ignition gets used over fuel. Also I didn't buy a quick-shifter but rather just used the programming inside the power commander with a button instead of the shift pressure sensor.
The different types of sensors and kills could be part of the reason for the time differences.
I also have the heavy 03 flywheel, heavy stock wheels, longer chain, ect. not sure how much this stuff effects shift time.
But I do know that with my set up a 90ms kill between 1st and 2nd would get neutral almost every time. And 90ms between 2nd and 3rd felt like it barely clicked in.
I also 100% agree with you about race pace. I'll bring my laptop and if everything feels good Ill try 95ms or lower at the next drag.
Is there anything wrong with a long kill time for shifting other than being slow?