According to Wikipedia:
In diagrams, the fact that an angle is a right angle is usually expressed by adding a small right angle that forms a square with the angle in the diagram, as seen in the diagram of a right triangle (in British English, a right-angled triangle) to the right. The symbol for a measured angle, an arc, with a dot, is used in some European countries, including German-speaking countries and Poland, as an alternative symbol for a right angle.
Note that it talks about an arc with a dot, not a square. For what it's worth, I've seen both "little square with dot" and "little square without dot" in Greece. I've never seen an "arc with dot".
I will be quite surprised if there is any particular story behind this notation. It is probably a matter of different communities using different notation for the same thing. Another example of this phenomenon concerns, e.g., the Notation for intervals.