VW go on the base chassis design.
What we call the Mk3, Mk5 and Mk7 on this forum are essentially facelifted (sometimes heavily facelifted) versions of the previous model. Hence the 'Phase II' bit.
Doesn't really matter so long as you make it clear what you're ordering parts for!
As dubious as Wikipedia is, it breaks the models down quite well
http://en.wikipedia.org/wiki/Volkswagen_Polo