I'm having a little difficulty picturing what you have. What it sounds like is, that nipple sticking out is the line to the transmission heat exchanger inside the end tank of the radiator and the nut is just to hold it in place. You start trying to turn that and you are going to screw up the heat exchanger inside the end tank of the radiator and effectively turn your rad into junk.
Go down to the hardware store and buy the proper "thread file", dress the threads. Maybe buy a matching compression nut (off the tubing) just to check fit and how the threads are working, before you try to put the tubing and nut back on there.
I've noticed the position of the tubing outlets are a little different on some replacement radiators. You can gently bend that tubing to fit, being careful not to kink it. Trying to force it, using the nut to pull it up straight and tight, is likely to be a no go.
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