Hi dastur,
There are far too many unknowns and variables involved in the different options you are considering and your design is much too complex to be able to predict the outcome of different configurations and how they will interact with your body type and sleeping style with any certainty and the only way to know the effect of changing the layer thickness will be based on your own trial and error and experience. Of course you can always start with 1" and then add additional inches if your experience on a particular combination indicates that it would be helpful although two or three 1" layers can also “act” a little softer than the same type and ILD layers in a single layer of the same thickness so you may need to take that into account as well.
In very general terms … changing the thickness of a middle transition layer will increase the pressure relief and secondary support of the mattress and will also change the “feel” of the transition between the top comfort layer and the bottom support layer while it will decrease the firmness of the primary support. Adding additional thickness to a mattress can also change how quickly a mattress becomes firmer with deeper compression and how well it adapts to different body types and sleeping positions (see post #14 here for more about the effect of thickness).
There is also a little more generic information about different types of layering in the “putting the layers together” section of the site, more about primary support, secondary support, and their relationship with pressure relief in post #4 here and post #2 here, and more about the some of the different specs that can affect the outcome of your design in post #2 here that may help you “imagine” the effects of different types of layering changes on the feel and performance of your mattress but in the end you will need to test them in “real life” to know the effects they will have on your specific application and design because the differences you are considering will have a different effect on different body types and sleeping styles.
Phoenix