Much to my surprise, it would appear your X99 motherboard does indeed have a 6-pin header marked EATX12_1 which
is compatible with a 6-pin PCIe power cable normally used with graphics cards. This would probably explain why the 6-pin mobo header is "keyed" to fit the 6-way PCIe powercable.
The other two 8-pin headers EATX12V and EATX12V1 both have their +12V pins on the opposite (normal) side, i.e. they conform with the EPS12V standard keyway pattern.
My guess is the motherboard designer needed three +12V feeds and since most "standard" ATX PSUs have only one or two EPS12V power cables, they decided to use a PCI Express (GPU) cable for the third mobo input. Unusual, but understandable.
CAUTION
If you match up the yellow (+12V) wires in the ATX PSU connectors (see link below) with the pins marked +12V on the three motherboard headers (page 1-37), i.e. EATX12V, EATX12V1 and EATX12_1,
before applying power, you should be good to go. If you have any doubts, seek further advice.
https://superuser.com/questions/849...nce-between-8-pin-eps12v-and-pci-e-connectors