I think the only time this issue becomes a problem is when it's interferring in your life. For example, your child can't get ready for the bus in time because he is trying to get everything lined up just perfectly <breathe> and he has to spend all his time 'fixing' things so they are 'just' right, <breathe> so he can't even get out of his room to brush his teeth and eat breakfast because he's trying so hard to get everything just right <breathe> so his day will go well, because if he doesn't leave everything lined up perfect his entire day will be off kilter <breathe>. Know what I mean??
easy child has always lined things up and organized her halloween candy by color, size and then type - in that order. I organize my book shelves so that they go in size order. Each shelf only has books with similar topics and yes, it bothers me when H stuffs one of his books in with mine. My hand towels must be folded a certain way or I have to refold them, etc., you get the idea. Does this waste my time? No, not really. Does it interfere in my life? No, not really.
Incidentally (and ironically), difficult child is a hoarder and her room has no particular order to it at all. However, if you ask her, she'd tell you that she has to have everything a certain way. It looks to me more like a tornado went through it, though she thinks it's organized. I will tell her, "difficult child, tidy your room" and she will respond with, "I did". lol
I think that if these traits are present and there are others that are causing stress or difficult situations in your child's daily life, then it's worth looking into.
I personally feel that lining things up or organizing things a 'certain' way are more like quirks and who among us doesn't have a quirk or two? But that's me. I think if you make a big deal out of nothing, it will become a big deal.