I don’t believe there are any energy code mandated requirements for the shared floor/ceiling in this scenario. The energy code only mandates requirements for raised floors that separate conditioned and unconditioned space, which is not the case here. This is likely why when you test different insulation values, it makes no difference. There is no requirement for insulation here based on energy code. However, it is likely a good idea to have some for sound mitigation.
Since there is no requirement, you do not have to input this surface in the lower unit’s energy model. As far as I’m aware, putting this in as an interior surface on the lower floor will actually add additional floor area to the unit, which is incorrect. There is no way to model a ceiling only, it must only be modeled as an interior surface ceiling/floor on the unit above only. Check your lower unit’s model floor area on the CF-1R and see if it is double counting the area because of the way you’ve input the ceiling in the model.
For your ductless system, make sure to select the system element, distribution tab, and specify the heating distribution and cooling distribution. This is where you specify your system is ductless, not by selecting the system type at the system input. See attached image for reference.