I guess it's all a matter of perspective.
I admit I also don't understand how marking the base of the hoof, which you can't see, is really that offensive, if you're willing to replace the whole mane.
But it is personal perspective. For me the pony that started this discussion is pretty much worthless. Obviously in real terms she isn't, but for me she is. If she had her hooves written on but original hair, I'd value her much higher. I don't mind hoof writing, so I guess I am finding it hard to figure out why it's so much more of a problem than the rehairing.
I see both rehairing and marking a pony as doing damage. It doesn't follow that damage is negative, necessarily, but it is still changing some part of the original. I personally believe if you aren't willing to mark a pony as a rehair (or a repaint), you shouldn't rehair (repaint) it. But that's just my view, and I accept other opinions exist.
I personally do care about who has my ponies after I die, and that they are happy with them. It may not be my problem, but I do care. And I do care that something I do to a pony may affect someone else in the future, which is why I don't use chemicals on ponies either.