Aha! I figured it out. There are other objects taking up that space- rather, the ghosts of other objects.
If you set the regularization factor to 0, you get the shape outlined in green here; when you overlay it against the DAPI image, you can see that there are some partial nuclei there (and I confirmed in IdentifyPrimary that they were there and had been discarded because they touched the border.) This happens whether they're thrown out for size purposes, for touching the border, or just when they hit your filter for CYTO intensity- they're still claiming the space.
I'd have to give some thought as to whether IdentifySecondary refusing to overlap with objects that have been removed is actually a bug or a desired behavior, but it's an explanation at least. Setting the regularization factor to 0 will at least allow you to get most of the cell.
Edited to add: Aww, man, @Anne_Carpenter, stealing my aha moment like 5 minutes before I finished typing up the post? Not cool.
Also, I've filed a GitHub Issue to see if people agree whether or not this is a behavior we should change; if so we'll get on it.