yes, they both come to a stop but the way they come to a stop is different.
the newer gear has the clunk.
the older brass gear has no clunk.
what does your camera do at the end of the cycle?
well this is an old thread, and OP seems not logged in anymore since 2017, but it popped up in a google search I have just done about serial numbers of the S2.
I found a body for sale, the seller describes it as a late S2, yet the serial is in the 160.000, the knob with the black crank and not conical. So it is in fact a S2A despite lacking the S2A mention after the serial digits (which is mentioned elsewhere as being done by Bronica for later models, past the 150.000 ones).
but reading through this thread I found very strange the comment about the older S2 making no "clank/clunk" noise winding/cocking. I have a low serial S2 (CB 7x.xxx) with conical knob and plain aluminium crank, and it definitively does "clank".
I am also surprised that the "S2=inferior brass gears" myth was still floating around couple years ago. I am new to these Bronicas but did extensive web combing, included in japanese, about their mechanism, and no, the S2 winding gears are not brass. As show for instance on Pierre Dirapon site, it's all steel but the S2A has bigger gears/teeth. Obviously. pros who were shooting these bodies aggressively had certainly caused havoc in these small gears, but that's not because brass...
S2:
S2A: