The article isn't very good.

A keyboard is scanned by pulsing each row individually and checking which columns become active because a pressed key connects them. (Or vice versa.)

In (2), when the green row is pulsed, only the green column becomes active, because it's connected to the green row by the pressed key (upper left red dot).

In (4), when the upper of the two green rows is pulsed, both the green columns become active — the first because the upper-left red dot is pressed, and the second because there is a path through all three of the red dots (pressed keys). So the keyboard senses a key press at the dotless intersection, even though that key is not pressed.

Better keyboards solve this problem with a diode on each key, so that the roundabout path can't happen. Cheap keyboards rearrange the rows and columns into squiggly paths so that the three-key pattern doesn't happen very often, being especially careful with the modifier keys.

Presumably the different colors paired with "so long as the keys in question fall into mutually discrete columns and rows." means they keyboard is actually "several keyboards" at the hardware level, and different keys activate different logic boards for processing.

Yes, actually, you can still determine the keys. The usual method is to scan the rows and/or columns one by one and then you always only have one row and column active at a time, so you can determine individual keys. However, if you strobe too slow you can miss keystrokes.