Hi,
I know what you mean...my lo has been an independent sleeper for a month now, and I feel like I can't do anything, or I am a hinderance to the process! I wish I had some advice for you on that one, but I do not unfortunately.
I'm inclined to agree with your point that he may not be staying asleep for that afternoon nap because he is getting enough sleep overall. While all babies are different and have their own needs, it seems like that is at the top of the scale for total sleep? I wonder if you cut the am nap down to 45 minutes for awhile, if it would help extend the afternoon nap. Maybe you could do this for awhile until he's ready to do just one afternoon nap? Or maybe you could wake him up an hour early, or put to bed an hour late (to essentially reduce the night time sleep by an hour)...maybe that would increase the daytime sleep to help him make the long alert stretches more happily. It seems from most of the things I've read that 12 hours is really more the norm for night time sleep. So, maybe you could re-arrange it all a little?
This is just what I would try out if it were me...but I am not an expert, so take my comments with caution! I'm sure you'll get some other input on here as well.
Good luck
katemom