Just for a reference for the OP about Polypterus Senegalus, I had 2, one was eaten by my redtail cat, but at the time of death he was 10", but here's the twist, he was only ~8months old, or at least I only had him for that amount of time, but he was only 2" when I purchased him from the LFS.
With that said, his growth rate suggested a much larger possible size than 10". He was on his way to at least 16-18" but has been housed in a 135g for the last 7 1/2 months.
As far as water quality and stunting of this particular species, I don't believe water quality plays a role per say.
Now I will say this with a disclaimer: I do not condone keeping fish or any animal in conditions falling short of perfect. Give all animals the best life and home possible. Ok with the disclaimer it of the way, Bichirs breathe atmospheric air, so poor water quality will not affect them in the same way as it would other fish. This is why in their native habitat they can survive for so long in stagnant, oxygen deprived water, and in extreme cases, leave the water to find more suitable water.
So as far as size for life, I believe they absolutely have the capacity to outgrow a 40b, but is it likely? Probably not.