Can I use 6+2 PCIe ATX power connector to power supply Arria 10 Dev Kit?

By PCIe 2x4 ATX connector, they are in fact meaning a PCIe 6+2 ATX connector like you would use for a graphics card.

They do not mean an ATX EPS12V connector (8pin CPU connector). Using a CPU connector would likely destroy the board.

You can see this from page 31 of the schematic (https://www.altera.com/content/dam/altera-www/global/en_us/support/boards-kits/arria10/fpga/a10gx_pcie_e3p1.pdf) - pins 1 to 3 are +12V, and the rest are connected to GND which corresponds to the pin-out of the PCIe 6+2 connector. The pins named "sense" on that connector in the schematic is a further confirmation as only the PCIe 6+2 has those.