I think the Bonneville gets closer to the "cafe racer" look of the Thruxton.
The T100, is a classic looking bike. To me, this is the furthest Bonnie from a cafe racer. A very cool bike, but all the racey styling cues are absent.
The Bonnie SE and Bonnie black are definitely much closer. Both sportier, but the SE has the lowest seat height of the line. Sporty looks, but standard ergos. A seat cowl and FEK, and you're practically there!
Last (and my favorite), the Thruxton. First, I don't know if this is true of the newer models but when mine was produced, it did have a slight hp advantage. Clip-ons or clubmans, swept exhaust, bar-end mirrors, seat cowl, racing stripe...For some that may seem a little "poser-ish" but to my eyes, it looks brilliant!