The decision to take Philipsen to the Tour and not Merlier was made before the season. Absolutely nothing to do with Merlier going to QS. Or well it might have had an effect on Merliers decision to leave but not the other way around.
I know arguments can be made about most selections and maybe it's not a good look to single riders out but still Movistar sucks hard for choosing not only Gregor Mühlberger but also Albert Torres over Mathias Norsgaard.
Lots of teams with mainly red jerseys do the Vuelta, and Junmbo ride lots of other races where the leader's jersey is red.
But even if the Giro organisers insisted, that should only be an excuse once: there is no rule that they have to have pink. So if they chose pink as their main colour, they were choosing that the Giro would be their one alternative jersey for the year if I were in charge anyway.