I had a similar issue with a late 2013 MacBook Pro retina. In the end what worked for me was:
# Disconnect the battery connector
# Connect the charger and turn on the Macbook
# Turn it off and disconnect the charger
# Connect the battery connector again
The next time I turned on the MacBook it recognized the iFixit battery. It was almost like it had to be powered on without any battery to then notice when the new battery was added. Funny enough, back in the day, I used to use this trick with 133MHz SDRAM when the PC wasn’t detecting a module.
Be very careful while turning on the MacBook with the lid open, you don’t want to short-circuit anything!