Toyota really did a nice job trying to "out-gun" Nissan with the mkiv Supra. The overall performance profile is awesome. In fact, I personally see no reason to spend $60k on a new E46 M3 if you have a 93-98 Supra TT.
You're right. The tranny itself shifts smoothly. The "clunk" comes on when you try to rush the clutch in 1st and 2nd gear.