Both Kindle for PC and Kindle for Mac don't have access to Personal docs archive (= book you've send via "Send to Kindle" app or e-mailed using Calibre or any other app/service that sends book to Kindle's email address), as in those books are not even visible withing PC app so can't be downloaded via PC app directly.
So you can't have Last-Page-Read and notes synced between PC and anything (Kindle device or Kindle apps for mobile OSs).
Not sure if PC apps would keep PDOCs in sync if you would : download the book on you Paperwhite and then connect it to you PC to manually copy the book file from PW's "Documents" folder to where PC app keeps downloaded books (was it Documents> My Kindle Content?)
I haven't used Kindle for PC since I've bought my first Kindle in 2010.
