Maybe it is for the trany but I thought I read somewhere on here that it was for the name of the motor... it also doesn't make much since to me to advertise the transmission on the engine..
I'm pretty sure it is the tranny... If the motor is called the Evo 5, than it would be because of the tranny anyway, but I've never heard of the Evo 5. Maybe I'm wrong.
The first generation of Evo Sporties had 4 speed transmissions, then in the early 90's they went to 5 speed units. Not much has changed on the Evos except heads and induction, and this engine has been around since 1984 in some form (BT and ST). The Twin Cam engines have gone through some changes (namely the "B" Balanced variant) for the solid mount applications.
I assumed it was for the 5 speed. Doesn't matter, 5 speed or Evo 5 it's crap and has to go. The company makes a ton of money on new timing and derby covers - all are grossly overpriced. But with the amount of money most of us sink into our bikes whats another few $?