Photos (and iPhoto and Aperture) use a database to store info about images, like faces. And other stuff. So does Lightroom and Capture One and many others. Using a database means you can store everything from image adjustments (like conversion to B&W) to metadata (like face names) in a database for quick retrieval, and it leaves the photos untouched. .... These are PIEs: parametric image editors.
Most PIEs leave your image files in place and reference them....So Photos, unlike most PIEs....
Well iPhoto, Aperture, LR and Capture One can all use referenced files as well as hod files in their own database. Capture One (not sure about the others), can happily do both at the same time (ie have part of your library in its database and part referenced).
Photos isn't feature-enhanced in this regard as you suggest. The fact that it is raising these questions on a pervasive technology and library implementation methodology implies Apple haven't implemented Photos particularly well. The is no confusion in Capture One, no strange apparent (or real) storage space cost.