I think the thinner topper will keep you closer to the support layers of the mattress and should represent an improvement over the 3" topper.
A couple of ideas as some food for thought though …
A mattress is always a balancing act between the need to “allow” the lighter parts of the body (such as the shoulders and upper body) to sink in enough into the upper layers (for pressure relief) and “stop” the heavier parts of the body (primarily the hips/pelvis) from sinking down too far into the deeper layers so that your spine is in good alignment. If the upper body is “held up” too much by the upper layers or the lower parts of the torso and pelvis are “allowed” to sink in too far with support layers that are too soft or thick then the resulting misalignment can lead to back discomfort and pain (which is most noticeable when you wake up in the morning). The layering and design that accomplishes this “balancing act” will depend on the body type, sleeping positions, and personal preferences. As a general guideline … side sleepers need thicker softer upper layers. Back sleepers need something “in between” and stomach sleepers need thinner firmer upper layers for best alignment.
So “support” primarily comes from a combination of the firmness of the deeper layers and the thickness of the comfort layers (how far away from the deeper firmer layer you are) while pressure relief comes primarily from the softness and thickness of the comfort layers. This is why the comfort layers need to be “just soft and thick enough” to provide good pressure relief in the most “pressure prone” sleeping position (usually the side for those who sleep in this position) but more than “just enough” can put you too far away from the support layers and not “stop” your pelvic girdle from sinking down fast enough.
When you use a topper over a mattress two things will happen. The first is it will compress and in combination with the layers below it will take on the shape of your body profile. Softer toppers will compress more than firmer toppers. This “cradle” formed by the upper layers re-distributes weight away from the pressure points of the body. The second is it will “bend” into any softer foam below it. This “bending” will happen more if the topper is firmer than the layers below it (what I call a dominating layer) because the lower layers will compress more than the upper layers and the topper will “bend” into the compression (or any dips or soft spots) of the foam below it. This means that the surface of the mattress will be slightly less conforming and feel firmer (less pressure relieving) and you will have a more “on the mattress” feel than if you were sinking in to a softer topper even though the next layer down is still compressing. Many people who are taller and slimmer will prefer a firmer feel like this because they are often be “sprawlers” and prefer a more on the mattress feel with more freedom of movement.
The down side to this arrangement is that the recessed gaps are filled in a little bit less than if the topper was softer and the lighter parts of the body (such as the shoulders) may not sink in as effectively for both upper body alignment and pressure relief.
The odds are that with a thinner topper and also because it is a bit firmer … you will sink in a little less with your heavier parts (hips/pelvis) and reach the firmer support layers faster which will help with alignment. The only possible issue is that it may not “allow” your shoulders to sink in as far if you are a side sleeper.
I wanted to mention all of this because I noticed that you were speculating about using firmer toppers to improve support and support comes primarily from the deeper layers of a mattress (combined with the thickness/thinness of the upper layers) and not nearly as much from the firmness of the topper. You could have very firm support for example with say 3" of soft foam on top of a mattress with a firm support layer underneath it. Using a firmer topper will have less of an effect on support and alignment and more of an effect on pressure relief and surface feel. The thickness of the topper on the other hand will have a bigger effect on support because with a thinner topper your pelvis will have less room to sink down before reaching the firmer support layers which lets the support layers “hold up” the heavier pelvis/hips more effectively. An extra inch of soft foam in other words could lead to a more “supportive” mattress that keeps your spine in better alignment than 2" or 3" of firmer foam.
This is also why it’s not really possible (except to a limited or temporary extent) to improve the deep support of a mattress where the upper layers are too thick and soft (or have softened or degraded) or the support layers are too soft by adding a firmer topper because the real solution would be removing or replacing some of the foam which has softened or broken down with thinner upper layers (not adding thickness with a topper) or replacing softer support layers with firmer ones (which can’t be changed with a topper).
One final thought is that all foams and mattress components (including the cover) will soften or “break in” to some degree in the first few weeks and this is normal. Latex will do this less than other types of foam. Once the initial break-in period is done (usually over the first 90 days or so) … then any further softening will be much more gradual (and again latex will be less than other foams here as well).
Lower quality foams will soften more both initially and faster over time and break down sooner (develop soft spots and/or impressions) than higher quality foams. If any of your latex layers softened over the first few weeks (or worse yet developed an actual impression without weight on the mattress) beyond the normal “break in” process then it could be an indication that the layer was defective which would be very uncommon.