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Same issue on a two week old ender 3 pro.
Just finished printing and was having trouble getting the parts cooling fan to fit into the female slot. I am in the same boat as you. The little flange piece that is inside the duct that the older fan keyed into is not the same as on the 2019 Ender 3 Pro (and guessing non Pro).
I took a dremel to these nubs and it seems to fit ok. But yes the alignment on the duct with the screw holes given are m3 vs the stock m2 screws but i ended up making it work and the height was ok for me.