Having been the step-daughter as well as the step-mother on this issue, I can tell you if you make it a big issue so will your step-son.
Using your example, my reply would have been "I'm not entirely sure that is accurate. Next time, can you take a better look at the clock and let me know?" OR "Hmmmmm, oooookkkkk, what having you been doing with yourself this whole time?" The last one's answer will give you a better idea of how long he has been awake by what he has been doing.
Basically at this age, children in general are looking to see what lies/fibs you will believe. If you just voice the fact you know they are not telling you 100% truth but don't blow it out of proportion, they tend to slow down with the petty lies/fibs and eventually stop. Until they are teens, of course! LOL!
Using you example again, if you need to know what time he gets up so you can try to be alert to what he is doing for safety reasons, maybe your reply could be "I just wanted to know because I should have been awake so much earlier. And I thought if you got up before me, then you could help by calling out to me if I am not already awake when you get up."
If it just bugs you to no end and you need to resolve this, then sit down with the whole family and decide together what the consequences will be if someone lied/fibbed bout getting up in the morning versus having homework done. Some people just can't tolerate any kind of lie/fib and that's fine as long as the discipline is not the same for something petty and something more important.