I think most companies are pretty flexible on your arrival time. They know renters are at the mercy of the airlines. I've been early by an hour and late by 6 hours and it wasn't even a slight problem.
But they are VERY strict about the return time.
Also, if your pickup and drop off times are very different (one is morning vs afternoon), you can get some unusual proration a for a partial day. In fact anything more than a few hours usually counts as a full day.
I wouldn't sweat the difference in your times. I always pick my airline arrival time in case the flight is early. Does anybody else have a different experience?