According to C.04.3 FIDE (Dutch) System:
A.6 Colour differences and colour preferences
The colour difference of a player is the number of games played with white minus the number of games played with black by this player. The colour preference is the colour that a player should ideally receive for the next game. It can be determined for each player who has played at least one game.
a An absolute colour preference occurs when a player’s colour difference is greater than +1 or less than -1, or when a player had the same colour in the two latest rounds he played. The preference is white when the colour difference is less than -1 or when the last two games were played with black. The preference is black when the colour difference is greater than +1, or when the last two games were played with white.
and
A.7 Topscorers
Topscorers are players who have a score of over 50% of the maximum possible score when pairing the final round of the tournament.
and
Absolute Criteria
No pairing shall violate the following absolute criteria:
...
C.3 non-topscorers (see A.7) with the same absolute colour preference (see A6.a) shall not meet (see C.04.1.f and C.04.1.g).
Hence when "disable color check in last round" is set the colour rules are applied for those with a score of 50% or less but not applied for those with a score of more than 50%
The point of this is to allow players to play each other when this might affect the prizes.