Possibly Simple - How to harmonize multiple non-consecutive layers

I guess I could try and harmonize all aspects of the image against the background (I’m specifically referring to the [AI] harmonizing tool), this seems like a decent idea. I don’t know if there is anyway to harmonize multiple layers which make up the subject (because legitimately there are aspects of the image which I don’t really want to harmonize which are layered above part of the subject, while being layered below other aspects of the subject) even if those layers are separate and not directly above each other. I have read about converting to smart object, but that appears to put all the layers which are in between the subject layer in the subject layer,

If worst comes to worst, I will just flatten all aspects that make up the subject and other things, but I am wondering if there is someway to avoid this.