Just a theory, but it's possible that the 32-bit version uses single precision floats internally, where as the 64 bit version might use double precision floats for the calculations.
Single precsion floats have a precision to about 7 or 8 decimals, which could explain what you're observing.
You may want to retry using FME 2019, I believe some aspects of the EsriReprojector has been redone.