Hello and welcome to BW forums

At 3 months we'd expect the A time (activity, so time awake including feeding, nappy change, anything that is not sleep) to be around 1hr 20 to 1hr 30 so it looks like sometimes your LO gets this amount but other times he doesn't. You might have more success with naps if you watch the clock a little more and aim for the 1hr 30 A time between each sleep.
Reflux can be terrible for disturbing sleep though so even on a perfect A time LO can still wake because the acid is coming up, it's more uncomfortable to be lying down and can wake them when they need more sleep. If your LO is not medicated for this you might consider seeing the doc to discuss trying some medication to see if it helps as it seems you've been struggling with short naps for a long time now. Other things which may help are using a cot safe wedge or cot blocks to make an incline to sleep on.
If he falls back to sleep I would let him have a good sleep, he will wake when he is ready and/or when he is hungry enough to wake for food.
hope this helps, please feel free to ask more questions or for clarification.