You need to do level matching with a voltmeter at the speaker terminals using a test tone.
That difference can easily be felt from level mismatch - or even from cognitive bias.
Though I'm still guessing you have some DSP going on in the Sonos Amp. Having said that - despite it's excellent measurements I'd not expect the Topping to sound significantly better than the Sonos, which is also a good amp, and the topping has less power. So if you'd just asked the question "would the Topping be a good upgrade to the Sonos?" I'd have answered "Probably not"
EDIT - what happens if you use the same Wiim into the line in of the Sonos? (You don't describe the Wiim as being the source for setup B). And I assume you are not moving the speakers between tests - just changing what is connected to them?
(Also struck out the "more power" comment - was looking at the wrong Sonos Amp)