Just because there are a couple other models in the FSPort MVPs and in other mods that might like to use this trick, here's exactly what I discovered:
It's the radius and bounding box of the detail0 subobject, not the model as a whole, that matters.
The radius controls the size of the weapon as an icon: FSO seems to be trying to fit the model's radius within the height of the icon (this makes it tiny for the obvious reason). You can set the radius to an incorrect value, about 40%-ish of what it should be, to compensate for this. It usually took me a couple tries to make it look right.
Centering the icon within the rectangle uses detail0's bounding box. This is why the EMP bomb was so off-center - the detail0 is just the glass bit in front, with the rest of the model being a subobject of that. I extended detail0's bounding box back to cover the whole bomb, and the icon moved forwards to fit the rectangle.
Centering vertically is backwards, for some reason. Extending the bounding box downwards will make the icon move downwards inside its rectangle. A few of the models I tweaked have bounding boxes with the bottom bit moved in the opposite way to what you'd expect, because that made it fit correctly.
None of these tweaks to detail0 seem to change the way the model is displayed in its animation, on the side of the window, so don't worry about that.