I am not sure if there is a biological reason or not - I actually think it is more to do with custom and where in the world you live (hot countries - siesta in the afternoon). I know my DH would love us to have a sort of day where we all siesta and stay up late, but we live in Scotland, so not much chance of that happening here!
I guess you maybe need to think about some kind of compromise between you, your DH and your LO to get something that will work for you all - it may be that your LOs body clock will eventually adapt to a 'natural' 12 hours or similar a night and give up naps altogether or it may be that he will just start taking a later and later nap and still stay up late - whatever works for you all, in my opinion, is what you should do.
I think my daughter would 'naturally' get up at 7am, nap at 4 - 8pm and go to bed at 11pm or midnight, but that doesn't really suit us, so she normally goes to bed at 7.30 / 8 and gets up at 7. Not sure if this helps or not, sorry!