This is a legitimate example, but most of the harm goes away as sample sizes increase. The point behind the .44 coefficient is the percentage of FTs taken as the result of And-1s and Ts as opposed to ones from shooting fouls or bonus fouls. While that leaves room for quirks like the ones you pointed out, it allows one to estimate the TS% for every player in the league by just adding the formula into and Excel sheet of all the stat lines. If you were to actually have to look to see whether the FT was part of a used possession, the stat would be significantly harder to calculate (to the point that it wouldn't be used at all honestly).
It's not perfect, but it should give a near-perfect fit when taken in large samples.
This isn't all that great of an example. I mean, he missed more scoring opportunities. Of course his percentage should be lower. Again, though, that would be sorted out with a bigger sample size.