I think the concept is these filter functions are supposed to be unobtrusive so that we shouldn’t need to worry about what they do, that they should “just work”. As you might imagine, some types of users take offense when software presumes to know what they want better than they do. I totally get it, I tend to lean that way myself. What probably causes the most grief is the wpautop() that tries to guess where to place <p>
tags.
I’ve learned to live with it. How it affects layouts isn’t that critical for my normal content. It can be really annoying when it changes a very carefully composed composition. wptexturize() isn’t as bad, it’s more of a style thing that I’m OK with.
I neglected to mention there’s another filter function that strips out potentially harmful HTML tags. It is suppressed for admins and editors, so it’s unlikely to affect you, but it could frustrate lesser users.
One last thing that relates to your other topic, while I have your attention. While it’s true we try to keep these forums clear of unnecessary topics, that’s not the reason we send people to dedicated theme support. That is because we cannot possibly know all the themes very well. The theme authors are generally the best people to answer such questions since they know their themes better than anyone. Of course, if theme authors aren’t responsive they’re not much help.
Ideally, people would ask first in the dedicated forum, and if no response is forthcoming they could then ask again here, explaining the situation. Each forum gets a different audience so their experience will vary. Very few people do what’s ideal, and that’s fine. We try to direct them to the best location to get a good answer, even if it’s stackexchange ??