There are some restrictions because of this. One is that per display scaling is unsupported in the worst case, or a hack in the best case.
Another is that the virtual display is always a rectangle, meaning that if you have different resolution displays, you end up with some parts of the canvas not being displayed anywhere. Most window managers and desktop environments know not to place window contents or UI chrome there (like panels), but the space is still there, and you can see this when using screenshot utilities which simply write the whole canvas to a file. Your mouse pointer can also hide in these invisible sections.
Getting X11 to display content on video outputs located on different video cards from different vendors can sometimes feel like a dark art, but other than that it mostly just works.