Interesting observation, I also play this etude, now almost daily, and did not notice this yet. I have the repeating sections memorized so I don't look at the score anymore for them.
The only reason why the two sections you mention could have different fingerings may be perhaps because the dynamics are marked a little different And the first chord of bar 16 and 43 is not the same, the one in bar 43 misses a note, but that would be quite a puzzle to start guessing why it misses that note, and if that note being there or not has influence for the change of fingering 2 half bars earlier.
One thing that helps me with this etude is memorizing. When I memorized the first two pages, I can study more focussed. Now still two pages to memorize, which has a lot of notes in common with the first two pages.
When I started playing this etude I also found the fingering awkward, but I also read that chopin's is already well thought of by chopin himself, so I started to memorize using chopin's fingering, and gradually I feel more comfortable with it. Ok I cannot play it on 144 yet, but I feel comfortable for a large part of the piece on about 100 with the metronome. Yet I already play it for 5 months now, so it takes time.... And I am not there yet.... In the meantime I try to enjoy studying it.