I wrote the original burst calculator on which the HabHub calculator is based.
Re: ascent rate. Here are the ascent rate profiles for 3 identical flights (same payload, balloon and fill) - as you can see they are pretty different. Identical Flights
I think unless you can predict which profile your going to get your probably better off not over-complicating the modeling.
Re: scale height vs air density model - your correct it's similar. But the air density model value is empirically derived from balloon data and includes factors like the constraining effect of the latex envelope.