Change 1 slide size and not the other slides

Unfortunately not Fred - it is the 'story size' and affects all slides in the project. You could perhaps work with the slide masters to try and achieve what you are after but we'd need a little more information on what you are trying to do.  

I stumbled across this as well; I was thinking to use the lightbox as a popup menu, which is to be called from multiple slides, since the lightbox by default already 'pop up' in the middle of the screen, would be perfect. But unfortunately, I can't change the size of the pop-up. 

The slides are all portrait, but I want the pop up to be landscape and slimmer. 

So then how are people lightboxing slides that are smaller than the slide underneath it?

To shrink the lightboxed slide is part of the built-in lightbox function.  You call it; the system does it.