don't fix those muscle to muscles intersection, this is not an issue.
to import the fat layer on the muscles layer you need to use the ziva builder API and import your fat exported but not applying the zBones
path = r'yourpath\fat.zBuilder'
import zBuilder.builders.ziva as zva
z = zva.Ziva()
z.retrieve_from_file(path)
z.build(bones=False,
tissues=True,
attachments=True,
materials=True,
fibers=True,
cloth=False,
fields=False,
lineOfActions=True,
rivetToBone=True,
restShape=True,
solver =False)