I'm not sure we've answered your question yet. As Leo said, layers won't help you with this issue.
In general, the order of the components in the component tree and the individual combine modes will affect how changing the base height of a component changes the others. The components add to each other from the bottom of the list to the top. So, for example, if you have a .25 thick component as the last item on the list, and everything above it on the list has a combine mode of "add", then adding .125" of base height to the item at the end of the list will add .125" height to all the others sitting on top of it. If you move this item to the top of the list and change its combine mode to "merge", then changes to its base height will not affect anything below it on the list. You can change the order and combine modes of the components to get them in the relationship you want.
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