At this age I still did, mostly because I was worried about sensitive skin and him getting a rash. I stopped doing it for pees around 3 or 4 months, if I recall.
I don't think it's unsanitary, though, and if he's not having issues with it I guess it's not a big deal. Could you change him once in the middle there somewhere? I used to change in between sides so he'd still be nice and sleepy when he went back down.