Thanks for all the replies. More info:
That's my understanding, as well; indicated speeds are taken from the drive sprocket speed. Speedometer interprets speed from that figure, with 6 formulae (1/gear.) That's why I was surprised at the indicated results, which I listed in my OP.
What I mean by "indicated speeds" is simply what the speedo is stating. I repeatedly checked these figures, before and after the sprocket swap, so I'm confident that they are accurate. I'll do a GPS check, this weekend, but didn't do one with the 46t sprocket, so won't be able to compare, without swapping back, which I doubt I'll do.
I replaced the chain, along with the rear sprocket and yes, it is shorter than the prior chain.
Figures aside, I am satisfied with the results. Less shifting in traffic and highway cruising speeds seem to be in the less-buzzy 4,500rpm range.
PS. What "generation" is my 2012 650? Thanks.