I'm guessing that after his solids supper, maybe he isn't hungry enough for a bedtime bottle. Do you offer a snack after the 2nd naptime? Perhaps making supper earlier he would take the bottle at bedtime.
I wouldn't make bedtime later if he is getting up at 5:30 every morning, in fact now that I think on it he might not want that bottle because he is tired, if anything I would push bedtime earlier. We usually try for a 12 hour day and night or as close as possible!
Oh, and I think by 8-10 months I stopped the milk at bedtime and gave it earlier, it never affected her sleep at all. We did water in a sippy cup at story time instead.
HTH
Heidi