Hi,
While siphoning the beer to bottle (from a 20L carboy), I was always moving the hose from top to bottom following the beer surface level. I registered the fractions "top, middle, bottom" and labeled the bottles as such. My observation, with different types of yeast and in several occasions, was that the top-labeled-bottles were lacking full carbonation and the bottom-labeled-bottles were fully carbonated.
I changed my siphoning routine into having the hose constantly close to the bottom while bottling. I registered the fractions “first, main, final” and labeled the bottles as such. I observed no noticeable carbonation differences after bottling.