I'm pretty sure you need to flip the green channel. Best way to check is put a single light source in the environment and check if the highlights match up with the light source
CE uses X+ Y- Z+ so yes you need to make sure you have flip y checked in NDO2 since it is by default (as far as I know) X+ Y+ Z+. HOWEVER, if you take a baked map that already has Y set correctly for CE3 (say from default max y-) and add detail on top with NDO2 using the normal to NDO2 option, be aware that having flip Y checked will invert your base normal map Y direction as well when converted, therefore making it incorrect.
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Why?
Because default Y+ and CE3 using Y-.