A little more-
If I understand your question, it is OK to have a little room above her shoulders to the straps. Since you do want the straps at or above the shoulders, you can't avoid a little space above the shoulders in some cases. If they slouch a little, that will be exaggerated a bit more.
On the other hand, like Robert said, you don't want any slack at the point where the straps are on her shoulders. Some use the rule that you shouldn't be able to fit more than one finger comfortably between the shoulder and the strap in front, others say you shouldn't be able to pinch the strap away from the shoulder.
If she is getting marks from the straps on her neck, please don't buy an aftermarket pad of any kind. Some parents just make sure to pull the child's shirt up between the straps and neck. Some even take a very thin baby sock and cut the end off it, then put that around the straps as a very thin layer to add comfort. We don't want anything thick or padded between the child and the straps.
It sounds like she is in a gray area where the lower slot may be fine if she slouches or a bit too low if she sits up straight. I agree with Robert that a free inspection might be a good idea if you have concerns. As long as the straps are tight, she should be pretty safe either way until she grows a bit more to definitely need the next higher slot all the time.