Perks of working from home; ripped open the package and put it all together:
If you use the bearing that comes with the bike, it sits a little higher. That is the photo I have. If you swap out the bearing for the one that comes with the headset, it sits lower, less than 2mm. It still does have a space, but isn't as much of an eyesore as this looks.
I don't think it's a perfect option, but for me, it is the only way I can run the stem length I want on this bike, so I'm going to roll with it. I'm sure I could figure out a different bearing solution, but I know that this will work and be 100% safe.
If I find time to head back into the garage I'll take a better photo farther away of the FSA bearing with the FSA C spacer and top cap.