Yip. It's the best way to do it! I have built watercooling loops in the past that are tested and excess air taken out in less than 1hr. Just make sure you stress each joint by moving the tubing about and you don't need to leak test for 24hrs.
I'd guess the upside down rad has trapped an air bubble that will generate froth till its filled.
Can you tip the case on its side so the outlet barb on the rad is at the top and run it that way for a while. (+ check the res is sealed and it and the pump don't move about too much)
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