As a concrete example: the spacebar key has its behavior overloaded all over the place. Some people make their keyboard firmware turn holding down the spacebar into a modifier key. At the operating system level, modifier + spacebar often has a special meaning: for instance in OS X command + spacebar indicates "switch to the next available keyboard layout", but then later that shortcut was also adopted by the Spotlight search feature (recent versions of OS X change the keyboard layout shortcut to command-shift-space but for a few versions the shortcuts collided and the results were unpredictable). System-wide utility software (for instance Quicksilver) uses or at once point used command-space as a default shortcut to pop up its UI regardless of the current application. Then various applications want to interpret the spacebar in several ways, for example for activating a selected button or other UI widget, or for scrolling, or for entering a physical space character. Photoshop famously uses a held-down spacebar to switch the active tool to the grabber hand, with command-space switching to the zoom in tool and option-space switching to the zoom out tool; other design/image software followed Photoshop’s lead, but sometimes implements things a bit inconsistently, for example in Illustrator command-option-space is required for zoom out instead. In the browser, things really get gnarly, because the browser UI itself uses the spacebar for all three of scrolling (space = page down, shift-space = page up), activating UI widgets, and entering space characters in text fields, depending on the current context, and then certain in-browser applications/widgets try to reinterpret the spacebar, for example a video widget will interpret the spacebar as play/pause, or a game will interpret the spacebar as shoot or jump.
All of these layers are clobbering each-other, so that existing software is already incompatible with defaults set at other levels of the stack. But as a user, if I try to make any changes to how one part works, I’m almost guaranteed to break something at another level.
Perhaps worse, the application keyboard context often changes without making the change obvious to the user, so that moment by moment I often can’t predict precisely what will happen if I press the spacebar.
(And this is not limited to the spacebar: enter, tab, arrow keys, and most other keyboard commands change their meaning based on the context in inconsistent and confusing ways. Once you get to the terminal, as explored in the original linked post, you get all kinds of other inconsistencies with certain keystrokes which only work in some contexts but not others, and various duplicate keystrokes which cannot be separately assigned, and so on. But these problems are not unique to terminals.)