According to High-Def Digest, the Freedom discs came out as "hybrids" - single layers of DVD and HD DVD on a single side. Not many people bit, though, because the prices were well out of line with what Americans are used to paying - $40 SRP for single 25 minute episodes and Amazon wasn't giving...
I think that early on, combo discs were limited to single layers on each side (or at least, on the HD DVD side); I'm not sure which way Paramount went with the TOS discs. I think they were dual layer, but I'm not sure.