For the last decade the clones have been functionally almost the same as the "real" ones. (Early clones tended to be awful and hence promoted sales of "real" ones after frustrating users.)
One of the differences has been in the USB-Serial interface. The early Arduinos used a FDTI FT232 chip and then switched to an AVR chip. This is the reason for the extra 6 pin header. Most clones use a dedicated chip, with FT232, CH340, CP2102 and PL2303 being the most common.
Another difference is some clones have extra connections to some pins for serial and I2c There is no additional function - just more convenient connections.
The grid of four holes labeled JP2 are four digital pins (PB4 through PB7) on the atmega16u2 that are not being used. It is possible to reprogram the atmega16u2 to make use of these, probably easiest done by using HoodLoader2.
One set is for the atmega328p, the other for the atmega16u2.
So, on the Keyestudio Uno R3 That I showed in the photo linked in the first post, there are no ICSP2 pins? Does that mean that the Real Arduino has a possibility that the Keyestudio version does not? Or can it be utilised via different pins?
As oldcurmudgeon pointed out, the Keyestudio Uno R3 likely uses a different chip for the USB-to-serial interface, so it will differ from the atmega16u2 version.
The arduino uno with a "genuine" 16u2 for a USB/Serial converter can have alternate firmware loaded into the 16u2, allowing it to behave as (for instance) MIDI interface or Gamepad. The boards with hardwired USB/Serial converters (like the Cp2102 I think is in the board you pictured) cannot do this.