That does not need to be a problem for you. It's just a matter of Layer Intersection Group Numbers and Building Material Intersect Priority values. And there are some other options for controlling this as well.
Graphic Override Options, Model View Options, etc... several different ways to go about it.
I would start with the Layer Intersection Group Numbers and Building Material Intersect Priority values.
You may also want to use Stories as a way to keep the various floor plans separate. This will allow you to use Trace Reference Splitter without quite so many Layers and Layer Combos.
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