The only pony anatomy mistake that I ever point out when DA artists make it is when they make the rear legs bend like a human's. Other than that, I ignore any anatomical wonkiness for the exact reason you just stated - the show itself bends the rules for the sake of humor. See: RD's dance thingy from Mysterious Mare-Do-Well.
This here is a great example of why I love your style. It's a huge evolution on the original show's style and you actually take the anatomy into account unlike many other artists here that seem to work only for it to look good even if it doesn't make sense.
But I like your rambling! As for the weird anatomical changes they suffer sometimes for the sake of animations, they're still far better off than G3 where they had some really weird anatomy and grabbed stuff with their hooves all the time.