I plan on playing as the male SS, but if I customize the female one too, then play as the male, will her appearance be reverted back to the default one throughout the game, or will she keep her customized one?

Only 19 hours left... yes!

Whatever changes you make stick, and whoever you leave character creator as is who you will play.

Yes, if you make your man dark skinned with like hair and your women light skinned with light hair they will both keep what ever changes you give them. and your baby will have light hair for sure.