A common problem athletes experience when getting their muscle up is that they will land deep in the bottom of the dip. When you are at your deepest ring dip position, it is highly likely that you are only being held there by the flexibility of your shoulders. When we secure ourselves in any position just by our end range of motion or flexibility, it's more difficult to keep or maintain enough tension to move out of this position unassisted. This is why a ring dip from that bottom position is so difficult. Landing with your shoulders on top of the rings as opposed to being wedged in between is an easier position to keep tension and transition out of. Another example of this would be the bottom of a squat. If you went down to the absolute bottom of your squat you would probably (depending on the individual's flexibility) be able to feel yourself lose tension to the point where you could no longer support weight standing back up.
Another reason this bottomed out position is less than ideal is due to the increased risk of shoulder injury or shoulder pain. Not only have you lost tension in that bottom position, but you are depending on your shoulders to hold your entire body weight. If you used a kip to get that position, you probably got there with force and momentum. All of these factors increase your exposure to shoulder injuries. Also, if your shoulders aren't stable, there is a chance a ring will slip from under your shoulder in that bottom position while one does not, which could cause a traumatic shoulder injury or fall off of the rings.
It's obvious that no athlete intends to land down in their ring dip that deep. We understand that's all the athlete may be able to manage to score a rep. The solution to this problem comes with technique practice, a lot of ring exposure and mostly experience. Over time your body will become more efficient at creating height without unnecessary movement or extra energy expenditure. For now, focus on pushing the rings down as much as your lats will possibly allow and not transitioning too early. Try not to confuse this with letting your hips get too high or the pull or kip. Push yourself behind the rings for as long as you can to create the appropriate height.