I use a Wattbike Atom at home and a Wattbike Nucleus at work, there is about a 40 watt difference in my ftp between the two bikes. Both are new bikes. I thought a watt was a watt and it shouldn’t differ so vastly. Wattbike advertise ±1% accuracy. Can you offer your opinion please 
Contact Wattbike directly. They shouldn’t be different.
My atom is within 2 watts of my Assioma duos over 20mins…
But, there is very little you can do to affect it… you will ideally need to compare both using power meter pedals for wattbike…
As an aside, I always found the old wattbike pro quite variable with its output, but I’m also aware people have seen issues with their atoms…
As said above, need to speak to wattbike, but they will ask for a 3rd party device to compare the 2…