I.E. is it possible to make global changes in a "patch" form by using modular xml loading somehow?

Say, if I wanted to change how the Pyramid works could I use modular XML to just make a pyramid-specific change without modifying the root buildinginfos.xml in my mod folder?

That's exactly right. With the basic BtS system, you'll need to copy the whole entry into a module, whereas with the WoC system, you need only copy the tags you want to change.