What it means:
Referencing
@ex-bubblehead's post the missing SATA ports "were not present for a reason."
Could have been any number of reasons: Keep costs down, SATA was "new" and adoption rates unknown, adding more ports created design and footprint issues, evolving design standards/requirements, etc., etc. Who knows....?
On the other hand manufacturer's (motherboard designers) often try to think ahead. They may leave an open space on the motherboard for future use; e.g., additional SATA ports. They may even install a physical port and the necessary circuitry in anticipation of future changes and new firmware. Does not get directly used but someone does a hack such as you have been trying to do and repurposes things.
Sometimes designers' reserve pins and sockets for "testing purposes". But in reality those pins and sockets are simply placeholders that, if well thought out, can be used for a variety of possible uses. Common in electronics.
Implementing physical changes on motherboards usually takes place incrementally. Be certain that the initial modifications and changes work before going on to the next. Leaves room for future changes and recovery from mistakes.
And with any given motherboard being made in different locations there may be variations. A model number may remain the same but the version number is significant. There is a reason, in many cases, why you are often asked to provide a serial number. That serial number is likely coded in some manner to specifically identify a particular motherboard design and what features/functions are truly implemented.
The other lost aspect of all that is documentation - Configuration Management. If the paperwork is not kept up, not QA'd, spec's can quickly become confusing and contradictory. Product X may work for you but not for someone else with the same motherboard - different version. Or Product X was designed not to be backwards compatible (they want you to buy a new motherboard) but surprise it does works on some older versions.
So what it all means, unfortunately, that using the motherboard(s) for a 4 drive SATA dropbox server may simply not be viable.
It was truly worth a try and likely a positive learning experience.
However you never know: someone may come along, read this thread, point fingers at me, laugh, and post telling all of us just how he (or she) just created such a dropbox server last week.
I can live with that.