The Ferrari, IRL, has a dual-clutch transmission. The 'seamless' is used to describe it because instead of an instantaneous de-coupling of the transmission to the engine with a traditional manual clutch shift, or an automated clutch, the power is maintained without interruption, with the gearshifts overlapping while one clutch is released and the other is engaged.
There are a large number of cars with such transmissions now: TT's and most performance VW, Porsche 911's, BMW's, nearly all Ferraris, even the new Ford GT500 Mustang and Corvette have DCT transmissions, all of relatively similar functional design.
I don't know how the game accounts for this, to be honest... requiring "Manual Transmission" shifts is a separate technical detail... deciding 'when' to make the shifts, versus whether the game is actually simulating MT types or actually just controlling the timing of the DCT or whatever the actual type of transmission each model has.