Intel and HP both recommend having the SATA emulation BIOS preference set to RAID + AHCI whether you will ever use RAID or not. HP workstation builds come from the factory with BIOS set that way.
It is one of those unusual BIOS settings that affects what drivers gets installed during a clean install. If you have things set to IDE Separate during a clean install, for example, you don't get the necessary drivers for best SATA/SSD performance.
So, for me, I only use a modern SSDs (or a PCIe M.2 SSD in PCIe interface card) as a boot/applications drive in our ZX20 workstations. I never use RAID. This is a fine approach, and by clean installing this way I could add in RAID later.
Regarding eSATA, I use SATA port 4 for my eSATA backplane adapter attachment because it is more towards the front of the case and is easier to route the interface cable around the lower of the two PCIe video cards we use. There used to be some HP advice on what SATA port to use for eSATA in these, but that went away with later BIOS revisions. The ports will autonegotiate eSATA just fine. So, use either SATA port 4 or 5. Remember that there are 6 total SATA ports and port 4 equals the 5th and port 5 equals the 6th in the series. Ports 0 and 1 are SATA generation III; the others are generation II.