The major difference between the PCIe 3.0 x4 M.2 slot on the motherboard is that it uses a direct link connection to the CPU, whereas the PCIe x16 NVMe adapter utilizes the motherboard chipset to negotiate with the CPU. Utimately, the NVMe direct connection to the CPU results in slightly lower latencies - though for most applications and moderate users, the difference is fairly unnoticeable. As for actual bandwidth throughput, neither solution will utilize their full potential as the bottleneck will be the M.2 NVMe SSD itself. The fastest M.2 NVMe SSD doesn't come anywhere near the maximum bandwidth of either solution.