The reason -in my eyes- is likely the orientation of the piece in question that has the sticker on it. Like when you are solving a 4-color mastermorphix the small corner piece that sits in the center of each color can be rotated wrong, resulting in the puzzle not being solved and you having to do another sequence of moves to sort it out.
You don't see this while solving because there is no up or down to be seen, however suppose there is a sticker on it of which you KNOW the bottom is facing a certain color, then you'd know the piece was rotated incorrectly were it facing another color. As you see this happening while you are solving you can take countermeasures and correct it and thus you MAY have an advantage over other cubers that don't have this sticker because it saves you time.
The fact that only one sticker max is allowed on any and all cubes, I think, is that they have to make a sweeping rule about this, otherwise as the Dutch say "is het einde zoek". Roughly translated: you can keep making exceptions for this cube, and exceptions for that cube, and you can keep doing this every time a new shape cube that is entered in a competition comes out. Very time consuming, and very annoying to adapt the rules all the time. Hence the sweep.
I could be wrong, of course, but this is why -I- think this rule is there.