"Special" covered a lot of variations from the "standard" offering including but not limited to tuners, a non-standard finish color, or more complicated work such as mounting an F50 neck on a D50 for Tommy Smothers in '63 and calling it a "D50 Special".
Typically they were "special ordered" by the customer to obtain a unique spec, like the ornate neck of the F50 on the "mid-level" D50 body.
Other details might include special fretboard inlay, and special bridge/fretboard/neck wood.
Some "specials" were built just for the sake of experimentation or to "dress up" stock models without having any specific customer order.
Also, the labeling and tracking of specials wasn't rock-solid consistent.
In the early '80's Guild did introduce some models that didn't lend themselves to "simple" left-hand conversion. Some price lists from the era and into the '90's list a standard fee to order left-hand versions of most flattops and hollow/semi-hollow bodies, but a couple of models were specifically exempted from left-hand versions, like the Songbird. It had a solid routed body and flattop. I suspect setting up a reverse jig for the body was cost-prohibitive, but there may have been other issues as well.
Another example from that time (mid '80's): when the F45ce was introduced, left-hand versions had to be special ordered. I could see a lefty F45ce from that era bearing a "special" designation just for being left-handed, as
@mavuser pointed out.
Y'got my curiosity up! What model/vintage do you have?