I have that issue on every single pair of sacai waffles lol. It bugs me a lot because I have mild ocd and when I tie both the laces together, one color loop is shorter than the other. But honestly, theres nothing I can do about it than to ignore it. But yeah re-lacing every single pair of waffles, I've always noticed 1 color being shorter than a different color.
EDIT: I just realized you're talking about the laces being too short in general after using every lace hole, yeah its a tad bit short but I like smaller tied laces so it doesn't bother me so much.