While “theory at a distance” where I only have limited information about what may be happening (I can’t feel what you feel or see you on the mattress) often can’t provide the best suggestions … I can at least provide you with some possibilities that may be worth exploring and may “match” your symptoms. The first step is to see if you can identify the probable cause of your discomfort and pain.
In general … back pain and discomfort and in many cases joint pain and discomfort is most often caused by a mattress where the support layers are too soft or where the comfort layers are too thick and soft for the needs of the person sleeping on it. These are generally alignment issues and in the case of combination stomach/side sleepers it is a common issue because a mattress that has thick enough comfort layers to provide good pressure relief on your side will often be too thick and soft to provide good alignment on your stomach. The goal here is “just enough” thickness and softness in the comfort layers to provide adequate pressure relief because thinner and firmer comfort layers will generally reduce the risk of stomach sleeping.
Pressure relief and alignment/support are really opposites and conflict with each other. Pressure relief needs enough softness and thickness in the upper layers to “allow” the pressure points such as the shoulders to sink into the mattress so that other areas of the body can bear more of the weight and redistribute pressure. Support/alignment on the other hand needs “firmness” (mainly in the deeper layers) in combination with comfort layers that are thin enough to “stop” the heavier parts of the body (primarily the hips/pelvis) from sinking in too far in all your sleeping positions but particularly the more risky ones. Each of these has a range of layering that may be suitable (depending on the sensitivity of the person to pressure issues or alignment issues). The goal is to find a mattress where these two conflicting needs overlap and provide both pressure relief and alignment in the same mattress.
The pain in your lower back suggests alignment issues that can cause either pain in the tissues or nerves connected to the spine or muscle pain because they are working too hard trying to hold you in alignment instead of the mattress doing the work. These types of symptoms are typically either from deeper layers that are too soft (and allow your heavier pelvis/hips to sink too far into the mattress and causing the pelvis to “tilt” and putting the spine out of its neutral alignment) or from comfort layers that are too soft and thick and allow your pelvis to travel too far before they are “stopped”. This is a particular issue with stomach sleepers who typically need thinner firmer comfort layers and firmer support layers. Because the support layers of the Nature are fairly firm … it seems to me that the thickness and softness of your comfort layers could be the issue here.
The upper body issues can suggest comfort layers that are too firm and thin to “allow” your shoulders to sink in far enough when you are sleeping on your side which can restrict blood flow and cause your limbs to fall asleep or tingle. If there is upper back pain it can also suggest upper body twisting to compensate for comfort layers that are too firm to “allow” your shoulders to sink in far enough or that hold them up too high relative to the lower back which can cause misalignment in the upper part of the body. Because your comfort layers are quite thick and soft (including your topper) this doesn’t seem to “fit” your circumstances.
In some cases … the opposite can be true with upper body pain and comfort layers that are too soft can also create a situation where you are sleeping in a more “hunched” position with either the shoulders too far forward or the middle of the back sinking in too far and causing muscle tension. It seems to me that this fits better with your situation.
One of the things that can also help with more extreme sleeping position combinations is a zoned support layer where the area of the support layers are firmer in the middle third of the mattress under the heavier parts of the body (reducing how much they sink into the mattress) and softer in the upper and lower third (which allows the shoulders to sink in enough).
Because latex is such a resilient material and has such a high compression modulus (it gets firmer faster than other foams as you sink in more deeply) … it has greater odds of working well without zoning for these types of combinations but some people will do better with an innerspring or a latex layer that is zoned with an appropriate comfort layer over it. Materials with a higher compression modulus than Talalay latex (such as Dunlop latex) can also help because they can start softer but them get firmer faster with deeper compression and can “stop” heavier parts from sinking in as far.
Because of your description of being “punched” up and down your spine … it seems to me that this is a muscle or spinal misalignment issue rather than a pressure relief issue. Your comfort layer/topper combination is also very thick and soft which also points to this as being the cause of your issues.
There really isn’t a “standardized” hotel bed but in general they will have some softer and less resilient comfort layers (typically polyfoam which is much less resilient than latex and has a lower compression modulus) over a firmer support layer or innerspring which may be zoned. They also will typically use a topper or featherbed over this to add to the comfort layers and extend the useful life of the mattress. I think that the comfort layers of your sleeping system is probably allowing your heavier areas to sink in further than a typical hotel bed.
So overall … it seems to me that the Nature with a 3" soft topper may too thick and soft in the comfort layers for your stomach sleeping and perhaps even for your side sleeping. I would also think that any thick soft topper (fast or slow response) may have the same problem (allowing you so sink into the mattress too far). 6" would probably be worse yet.
Have you tried the Nature without any topper at all? If not this would be my first suggestion and based on your experience with this (and how it differs from your current experience with toppers on the mattress) it may give you more insights into what may work better for you. If you do need a topper over the Nature for more pressure relief … it should probably be either much thinner for “fine tuning” or of a type (such as shredded latex or wool) which are less risky in terms of alignment than the thicker softer latex toppers that you are using.
Hope this helps … and if you do decide to try just the Nature by itself I’d be interested in how it changes your experience and symptoms and the feedback from a few nights on this (one night is not enough to really evaluate anything) may be very helpful.