Strange... What version of the Intel RST drivers do you have installed (Device Manager -> Storage controllers -> Intel Chipset SATA RAID Controller -> right-click -> Properties -> "Driver" tab)? I'm using the default v14.10.3.1041 that comes with the Surface Studio (out-of-the-box, and via the recovery image). If you are too, then you could try downloading and installing the latest version of the "Intel Rapid Storage Technology (Intel RST) RAID Driver" from Intel's website (which is v15.2.0.1020 as of this writing). Maybe that'll help??? Also, you might want to try using CrystalDiskMark v5.2 for your benchmarks (if you're not already).

Do you have Bitlocker/Encryption enabled on your Surface Studio? If so, that's probably what's lowering the read/write speeds on your 960 Evo Benchmarks. Try turning it off and then run your benchmarks again. In theory, the M.2 2280 PCIe connector and the 2.5" SATA III connector should be completely separate from one another, and so it shouldn't matter if you kept the original 2.5" HDD installed or not (i.e. the 2.5" drive shouldn't have any effect on the speed of the M.2 SSD even in RAID mode). Even though the Intel RST controller is configured in RAID mode, it will behave as if it is configured in AHCI mode when a RAID array isn't configured (i.e. when it's using JBOD).

Take a look in Device Manager and you will see "NVMe Samsung SSD 960" listed under "Disk drives", and you will see that it is indeed using Microsoft's NVMe driver. On the Surface Studio, the Intel RST driver is configured in RAID mode out-of-the-box (in order to support the stock "rapid hybrid drive"), which utilizes Microsoft's NVMe driver for NVMe SSDs. This is also the reason why you can't install the Samsung NVMe driver (i.e. since Intel SRT is in RAID mode, the Samsung NVMe driver, as well as the Samsung Magician software, can't see the drive). It'd be nice if Microsoft would provide a way for Surface Studio owners to switch their machine into AHCI mode, but I seriously doubt that you'd notice any real world advantage to doing that. The 1 TB Samsung 960 Evo in my own Surface Studio is reaching nearly 3,000 MB/s read and 2,000 MB/s write speeds with the stock Intel RST RAID mode configuration.

FYI: Detailed step-by-step instructions on how to "properly" upgrade the storage in a Surface Studio can be found over in this iFixit Answer Forum thread:

Does the Surface Studio supports PCIe SSDs?

Detailed step-by-step instructions on how to "properly" upgrade the storage in a Surface Studio can be found here:

Does the Surface Studio supports PCIe SSDs?

Please be sure to read through the entire thread as it contains lots of information (and warnings!) for folks interested in upgrading the SSD/HDD storage of their Surface Studio (both the Core i5 and Core i7 models). Enjoy!