Also I cant say I totally agree with these numbers either. Like, it just doesnt show how well each individual opponent played during the match. For example Nadal's win over Verdasco in the AO 2009 semi should be rated as difficult as his win over Federer in the final.
Well it rates how difficult it would be for the average player to win this, not specific instances of certain players finding great form within a tournament. For example, regardless of any ranking system (ELO, ATP, you name it), what would be considered brutal draws for the average player at Roland would be much more manageable for a player like Nadal who thrives on clay. Actually and according to the article, his three most difficult paths all have been at Roland-Garros (2012, 2013 and 2014). Context is appreciable in such instances. Likewise, Thiem's path at Roland this year is in the top 10 paths in terms of difficulty... even though for Thiem it's more manageable on clay than it would be anywhere else.
To make it short: this system considers how hard it would be for an average semi-finalist to get through, not how hard it would be for a specific player to get through.