ahaaa.... so if we'd use
www.paysite.com/index.php?id=1234, would google count it as
www.paysite.com/index.php ? - Cause if it would seem to google that all affiliates would be linking to the same page - index.php, index.php would get a better pagerank instead of it being divided by multiple pages... then again, a site's total pagerank is also measured by the number of pages it has, so which is better index.php having an excellent pagerank, incase the above ?id= trick would work, or the site having more pages and a total higher pagerank.
Third, if the site has more pages only due to wm code, the content would be similar/same, so there could be a danger of being penalized for that.