Purpose of extra holes for pins or Arduino clone
It's what they say they are.

SDA/SCL are I2C - what used to be A4/A5 on the old footprint. On the '328 based boards those are directly linked to the A4/A5 pins.

The blank pin isn't used. The 5V next to it is actually mislabelled and should be labelled "IOREF".

AREF has been there since the very first Arduino boards.

It's the standard "R3" Uno footprint, plus some extra breakouts for the I2C in different forms (probably to go with specific I2C devices they also sell).

All of that is on the Uno's product page if you'd care to read it some time...

The ones by the cheap Chinese USB interface chip will be something to do with that. Maybe RTS/CTS broken out on a header. You can ignore those - they are of no interest at all. In fact, just looking in their direction has a good chance of breaking the USB interface chip. Stay well away.