Theory - It is extremely likely that Krafft subjected Eddie to methods used by MKULTRA. Based off radios it's clear Krafft had good intentions despite the shadiness of it all, if this is true.

This would explain why Eddie in CW clearly has his memories of the Aether story intact (we know this is the case given he remembers Samantha's Birthdate/place) as well as gives credence as to why Eddie didn't have any scruples about subjecting his own adoptive father to torture.

Source for MKULTRA involvement: New Horizons audio log, Citadelle Des Morts