The Mac Pro drive bays have a SATA2 controller which has a maximum speed of 3GB/s or 300MB/s. The new technology SSDs are SATA3 which have a maximum speed of 6GB/s or 600MB/s.
SSD on the drive bay performs at 275MB/s.
SSD on the PCIe slot performs at 550MB/s. Installing the SSD on the PCIe slot allows the SSDs to perform at it's full potential.
An AHCI M.2 SSD on an PCIe card performs at around 1500MB/s and your Mac Pro will be able to boot from it, giving you full speed.
A NVMe M.2 SSD on an PCIe card perferforms even better but your Mac won't be able to boot from it, unless you're prepared to make some firmware modification (NOT recommended).