Normally it would be limited by the hub, as you described. There's a little ridge that the retainer bearing would hit and seat itself upon. Then you would install the spacer and then the opposite side bearing, which has no ridge to seat itself on (that's why it's "floating").
But in your case I am theorizing that you didn't get the retainer bearing all the way to the ridge, before proceeding to install the spacer and the opposite (floating) bearing.
So after you installed the retainer bearing and then the spacer, you probably tapped that floating bearing in just until it made contact with the spacer, which would mean it's one or two millimeters too deep. So right now, if you try to push the retainer-side bearing deeper until it is "seated" (stopped by the ridge inside the hub), then you will damage the inner spacer because it will get crunched between the two bearings. The inner spacer is thin and I do not think it's strong enough to withstand that driving force. Nor is it meant to be tightly crunched between the two bearings. I think first you have to push out the floating bearing so that you can free up some space to drive the retainer bearing the rest of the way to the ridge.
Aaron
PS: When I encountered this, the mistake I made was to use the old throwaway bearing as a pad to hammer in the new bearing (so that I wouldn't directly hit the new bearing) and then, unfortunately, only sink the new bearing to the depth corresponding to the width of the old bearing, which turned out to be one or two millimeters shy of the ridge. Sounds a lot like the issue you're having.
by the way, in this thread I've using "flange" and "ridge" interchangeably. Not sure which is more accurate, but I think you know what I'm talking about.