Althoug ArionFX works on 16 bits it is designed for 32 bits and you should always use 32 bit for it to work properly. So convert to 16 bits afterwards, yes. By the way, ArionFX will output a low dynamic image, it will still be in 32 bits but it is clamped after any action in ArionFX.
The important part is to avoid layer blending other than 'normal' if you want to switch to 16 or 8 bits without visible differences. Or, to be fully flexible, convert to 16 bits before you do your corrections.
The reason is that the math behind the blending modes produces different results and there's no way to make it look identical without flattening the image.