Everyone is different, every shooting situation requires a unique solution, so it really depends on you, the individual shooter.
you're shoulders should be level as well as the bore should be as level as possible.
The idea of "as low as possible" is a miscommunication of the thought that the "lower you are to the ground the better". Well that was used to described the difference between positions, Kneeling is lower than Standing, so Kneeling is more stable then Standing. Sitting is lower than Kneeling, so Sitting is better than Kneeling. Prone is lower than Sitting so Prone is better than Sitting, it's about contact with the ground. Here is the mis-communication, once you are prone, getting lower doesn't make you more stable. You already have maximum contact with the ground. So mistakenly some people think, even in the prone you need to get as low as possible. This is false. It creates more problems than it might fix.
You need to comfortable, which is determined by our body type. You need to eliminate angles, and dipping one shoulder lower than the other is an angle. If your bipod hops or moves after the shot it is probably because of an angle which is usually because of a poorly adjusted bipod for your body type. Neck strain is a result of a poorly adjusted bipod, usually because someone is trying to get too low. The rifle on your collar bone in an uncomfortable way, try raising the bipod, you're probably too low which rolls the shoulder pocket down.
Get level, get square, get straight, which has nothing to do with low... you already have max contact with the ground, you cannot increase it. Find the best position for you, not because someone else incorrectly says lower is better.