This current (unexpected) behavior of the new 'one-time' color picker called from the button in 'Fill & Stroke' tabs had been reported in the comments of this (otherwise not directly related) feature request:
- Bug #1049481 “Allow dropper tool to edit current custom swatch fill”
https://bugs.launchpad.net/inkscape/+bug/1049481 and (kind of) got stuck there (i.e. not reported as separate item, nor added in the comments of the more relevant original request(s)).
I have added a patch in the original bug report [1] for the 'one-time' color picker in the 'Fill & Stroke' dialog so that : a) The Stroke page 'one-time' picker always applies the picked color to the objects stroke (with any key modifier). b) The Fill page 'one-time' picker still works in the same way in that you can pick either Fill, or Stroke (with <Shift> key).
Does that make sense ?