I personally enjoy the flawed wood. For shafts, it is true that shafts with sugar & mineral play better, not because they show the aesthetic flaws but because those characteristics were apparent in the tree. I have always said that sugar maple without sugar is not right, not healthy. I don't know a single builder who doesn't note the difference of stability, rigidity, strength, & memory between clean white shafts & "dirty" shafts. But for at least a decade the trend has been white shafts, because that's what people want. Luckily the trend is coming to a close & it's becoming more acceptable for cue makers to use less than beautiful shaft wood again. Some players even ask for it.
As for butt woods, I don't mind the defects, personally. I enjoy the character. But with certain situations, like Brent's cue or the top cue I showed, the flaw breaks up the uniformity of the appearance. If there were several more of those marks, then it would be really cool. But the one mark on it's own looks out of place. I don't personally mind, but some buyers do. And I cannot fault them for it. So a new cue is a very viable option. In the case of a dealer cue, it's safer to just build a new cue than chance the end buyer not liking the mark.
I'm going to start using a lot of "character" woods. I have quite a collection of woods set aside that just don't look like the other stuff. It's not ugly, just has character. A rustic theme, for lack of better description.