It turns out that these clauses have been part of the rules since 2001, but were only included in the handbook this year (I have no idea why btw). But now that they are there what do they mean?
I asked this question of the Chairman of the FIDE Swiss Pairing Program Committee, Christian Krause. He said that what these rules do is deal with the case where a player hasn't played the same number of rounds as other players in the same score bracket (through byes or forfeits). For example, in pairing an even numbered round a player may have played an even number of games (eg only played 4 of the previous 5 rounds), the players mild colour preference (ie opposite the last colour played if they have had 2 whites and 2 blacks), shall be used to calculate x (the number of pairings in a group that do not satisfy all colour preferences), rather than treating the colour preference as 0 or undefined.