The 2x2 pin JP2 is connected to the Atmel 16U2 or 32U2 processor (whichever the manufacturer used) which provides the USB I/O interface to/from the Atmel 328p, the one we usually consider to be the Uno's processor. When pins are actually installed on that pad, jumpers may be placed across either or both pairs to connect the xxU2's pin-4 to pin-6, and/or pin-5 to pin-7, which connect to that processor's interrupts (numbered the same as those pins).

My searches have not yielded any answer to the question of why it was provided, other than to suggest that they may have been intended for a feature that was never implemented. You can see JP2 and its connections to the xxU2 processor in the center of this schematic.

The 2x2 pin JP2 is connected to the Atmel 16U2 or 32U2 processor (whichever the manufacturer used) which provides the USB I/O interface to/from the Atmel 328p, the one we usually consider to be the Uno's processor. When pins are actually installed on that pad, jumpers may be placed across either or both pairs to connect the xxU2's pin-4 to pin-6, and/or pin-5 to pin-7, which connect to that processor's interrupts (numbered the same as those pins).

My searches have not yielded any answer to the question of why it was provided, other than to suggest that they may have been intended for a feature that was never implemented. You can see JP2 and its connections to the xxU2 processor in the center of this schematic.

Update:

I was looking at the 3-pin connector(?) marked '???' in your question, and JP4 on the schematic in your update. Since your schematic does not show the xxU2 chip, and the connections of '???' are marked D11, D12, and D13, I'm going to guess instead that these are either auxilliary pins to access the 328's SPI interface, or is showing half of the ICSP hardware programming interface (the 3x2 pin block just above the '328 on the schematic I linked).