OK, so it sounds like "SPECIAL" is a draftable ship class for AIs, but it is generally not used in custom missions (how about Taldren stock missions?). "R" ships are kept away from the player shipyards, but not necessarily from AIs. Neither should keep a ship out of a GSA player's hands. So, if you didn't want a ship to appear on the D2 at all, mark it as both "SPECIAL" and "R" to essentially remove it. If you want the ship to appear in AI hands, but not players' hands, then try "R." If you want it to be in the shipyard but not available to the AIs, then "SPECIAL" can work, as long as the D2 admin has a build chance set up for "SPECIAL." Of course, all "SPECIAL" ships will be priced and available under common modifiers, so a CA-sized ship in that group would be a better value than an FF.
Of course, any admin can change these two tags and the .gf settings to fit their campaign without having to make players use a modified version of your shiplist. They can also change the YFA/YLA dates to suit their needs. So, as long as you find what works for you, the admins can do their own availability tweaking -- you don't have to try to please everyone, at least.