Both the motherboards pictured above use the same PCI-E configuration for lanes from the CPU. They are hard-wired x16/x8/x16/x8 PCI-E 3.0, and bandwidth from these slots isn't moved around. The upside is that performance is at its best, as switching around bandwidth using quick switches (simplest method) can have a negative impact depending on the levels of switches, so this way all slots get the best performance possible. The downside is that current motherboards that offer their x16/x8/x16/x8 (pretty much all of them) configurations don't offer the ability to run x16/x16/x16/x0.
However, the motherboard on the left actually has two quick switches that move x4 from the last x8 slot between the slot and the U.2 connector on the motherboard. In fact, the only two reasons I have seen quick switches on an X399 motherboard are for switching bandwidth to and from a U.2 port, or next to a clock generator. Both the motherboards above also have an x4 PCI-E 3.0 slot, and on the board on the left it's obvious by the size of the slot, but on the board on the right you can tell by the number of pins inside the middle x16 slot (it's electrically x4 PCI-E 2.0 from the chipset), so keep an eye out or read the specifications.
Most, but not all, X399 motherboards also have extra power connectors that supply the PCI-E lanes with extra power. The PCI-E lanes on modern motherboards get their power from the 24-pin connector, as CPU power is typically isolated for CPU-only use on most consumer motherboards. If each slot is specified to supply 75W of power, a problem is created when 3+ PCI-E x16 slots are filled up with high power PCI-E devices, such as overclocked graphics cards. If you plan on running 3 or more GPUs and especially if you are planning on overclocking all of them, you should look for these extra connectors. They come in two varieties; the 6-pin PCI-E power connector on the board on the left, and as a MOLEX connector such as on the board on the right.
Most X399 motherboards also offer three M.2 slots, and they are typically wired to the CPU at x4 PCI-E 3.0. A few vendors have also decided to offer heat sinks that will help cool down the M.2 drives. The board on the left has one of my favorite M.2 heat sinks, as these heat sinks have a mass to them and they make installing the M.2 drive very easy. They not only guide themselves into the connector, but they also hold and guide the screw into the standoff. You should install M.2 drives when the motherboard is on its back, and before you install it into a vertical position in a case.
There are also vendors that cool M.2 drives with stealth heat sinks that look like chipset heat sinks, such as on the board on the left. There is also another novel method by using a specially designed unique riser card, which allows you to mount M.2 drives to either side vertically. The vendor that does this also puts the slot for the riser near the memory DIMMs, so you can use the same fans that cool down memory modules to cool down M.2 drives, or if you don't have one, the vendor also includes a fan mounting bracket for their riser.
You will also find U.2 ports on a few X399 motherboards, and they are all connected to CPU bandwidth (U.2 requires x4 PCI-E 3.0). However, there are two methods as to where this bandwidth comes from. On the motherboard on the left, the U.2 port shares x4 PCI-E 3.0 with the bottom-most x8 PCI-E 3.0 slot, while the board on the right, the U.2 port shares x4 PCI-E 3.0 with one of the M.2 slots. You should consult the manual if you are planning on using the U.2 port and other connectors, as there is no simple way of telling where the U.2 connector gets its bandwidth.
NVMe RAID is one of those things that Threadripper would thrive with, and while at launch it wasn't present, AMD has announced that they are planning to bring NVMe RAID support on September 25th, 2017. That is huge news, as then you can RAID all three of those M.2 slots, and even drives in PCI-E slots, and not be bottlenecked by the chipset to CPU connection. That is huge, and one of the coolest things the X399 motherboards will be able to do.
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