They are logically identical; it does not matter.
EDIT: A side note,
M.2 slots multiplex SATA and PCIe. In order to facilitate this multiplexing, the M.2 connector is usually pinned to a SATA port on the chipset and PCIe lanes on the chipset.
Many motherboards pull their 1x and 4x PCIe slots from the chipset as well. In some cases, the same PCIe lanes are used for both and a firmware setting is used to toggle between them (using the M.2 for PCIe may disable a 1x or 4x slot).
However, Intel's CPUs also have their own PCIe root ports which are independent from the PCIe root ports on the Intel Platform Controller Hub. The PCIe lanes on the CPU have faster access to the system memory, but since Intel's CPUs do not have integrated SATA transceivers, it's not possible to pin them out as an M.2 port.
That adapter could in theory permit an NVMe SSD to access the system memory through the CPU's PCIe ports rather than the PCH's PCIe ports. However, the performance difference would be nigh undetectable.