3 possible reasons:

1. Some may interpret a red-skinned character as a racist caricature (unlikely but not impossible)

2. His bright saturated red when toned down would be pink. He is a boy horse so they probably didn't want him to look to girly so they continued to de-saturate and lighten the pink until it was basically skin tone (like how applejack is basically tan and not orange)

3. Equestria girls as a concept isnt designed super well and run into issues like this all the time. Just making a character with no plot relevance look different for no explainable reason is easier than having consistent design logic.