Intel's X99/Wellsburg chipset integrates the clock generator directly onto the silicon of the big fat DH82031 PCH chip. This is heralded as a Really Important New Thing. It's supposed to make clock timing/sync issues less issuesome, reduce all sort of technobabble latencies and skews and jitters and hiccups, and consequently provide a stable uniform clock source all across the board.
Intel believes, and rightfully so, that the clock should properly be integrated within the PCH - directly interfaced to the main processor, which itself directly controls/addresses high-bandwidth PCIe 3.0 lanes and DDR4 timings. The PCH also serves as the central bridge/controller for all the SATA and USB devices, PCI 2.0 lanes, motherboard services, etc. Intel claims this approach offers maximum possible overall system stability, especially at highest clock speeds.
Asus/Gigabyte/EVGA/MSI/Asrock believe, and rightfully so, that the clock should properly be integrated to the motherboard itself - just like it's always been since the dawn of x86 machinery. Everything on the board, including the main processor and the PCH chipset and all the many things they service, is synced off the motherboard-mounted clock part. The mobo makers claim this external clock generator offers maximum possible overall system stability, especially at highest clock speeds. (And then, of course, they go a step further by extending the maximum/overclock speeds beyond Intel's integrated part spec, at least on their high-end stuff.)
They can't both be better, so which is it?
My experience with hobby-powered microcontrollers is that they typically include an integrated clock source (to offer minimum/basic functionality at lowest cost), but they can also interface with an external clock source (and gain higher performance through a little added part cost/complexity). I doubt this example has much relevance when compared to vastly faster, more powerful, and more complex X99 chipset/mobo componentry.