I am pretty sure both bearings are flush on my IP-057 and IP-036, (this is a Zerostack integrated headset), the washers go on top of the bearing, under the Neco cap.
I just pulled apart my my IP-036 last night as it was making a creaking noise, I cleaned and regressed the headset. On mine, the bottom bearing was a snug fit but did push in by hand, the top just dropped in.
Have you tried tapping down the top bearing? What does it look like with the shims, top cap, fork and stem installed?