RFox Is your disagreement that natural fingering isn't the easiest way of passing the thumb under the fourth? If so I'm curious about how you finger Bb Major (RH) or E Minor (LH). Do you still use the 123, 1234 groupings or have you dispensed with that method altogether?
Given that you also advocate we figure out what works for our own hands, albeit with a teacher instead of a purely systematic approach, I doubt you're suggesting that we should all learn standard (and inconsistent) fingering without trying alternatives and regardless of ergonomics. What am I missing here?
I was writing about scalar passages in general, which are rarely a full scale over several octaves. Usually there are changes of direction, leaps, etc. In such passages I try to avoid the figures that are not so comfortable for my large hands, if possible.
I'm not saying the standard scale fingering is the best. I learned it because my teacher taught it. Some scales have never been comfortable but I worked at them anyway because sometimes we can't avoid the uncomfortable fingerings. You can try alternative fingerings to make scales easier or smoother but deliberately working on a fingering that's more difficult can also be beneficial.
In pieces, I have occasionally used alternate fingerings. For instance, in the Rachmaninoff Étude-Tableaux in G minor, the fast scale at the end wasn't as smooth as I liked until I changed the LH fingering to be more like E-flat major and sudently it was much better. However, I don't think you really need to practice all the alternate fingerings to be able to do this in a piece. If you have practiced all the standard scales then it's just a mind shift and slight adjustment.