When the Raspberry Pi first appeared in 2012, the unique form factor suffered one complaint: poor placement of screw holes. In fact the first version of the board had no screw holes.
Screw holes are important because add-on boards for the Raspberry Pi came in all sorts of shapes and sizes, causing a few issues. For example, the Pibrella board was designed for a 26-pin GPIO and it had a rubber foot to stop it shorting out on the HDMI port when pressed. What was needed was a standard connection, so with the Raspberry Pi B+ in 2014 we saw a 40-pin GPIO and screw holes added to the corners of the board. This offered a consistent mechanical point to which boards could be secured using M3 standoffs.
This new standard was part of the HAT (Hardware Attached on Top) which saw EEPROM chips that would talk with the new 40-pin GPIO and enable configuration of the board. This then became the de facto Pi form factor and subsequent model B boards have followed this layout, enabling a board designed to meet this standard to work across the range of Raspberry Pi.