On a research perspective, do physical layer rules come under the term "wireless protocol"
I may not understand what you mean by "come under" but let's see if I can properly make the case for the answer at the bottom.

Physical layer and protocols are two different things. 

Simple example is what ham radio operators call CW.  Continuous Wave.  It means to send a signal from a radio transmitter to a receiver.  It is called a carrier wave.  It would sound like a long continuous beep.  The only information you can glean from it is that there is a transmitter that you can hear.  That is the physical layer.  

But then when you use a hand key to interrupt that transmitter's signal in a way that others can understand, then you have imposed a protocol (Morse Code) on top of the physical medium of radio via carrier wave.  AM and FM stations do the same.  They take a carrier wave and change (modulate) it in ways that can be understood after demodulation.  The medium is radio, but the physical layer is really the carrier wave.

Similar for fiber optics.  It all starts with a light beam going down a fiber.  In fact, it may be multiple beams of different colors.  Those are the carrier waves which provide the physical layer.  

The physical layer is the method of signaling.  Radio, cables of various kinds, fiber optics, etc.   

Here is a good article that explains what physical layer means

Protocols are the ways those signaling methods are used.  Like framing and addressing of packets for routing, then the information inside the packets, and onward up through the OSI stack.  

There are many wireless protocols like WiFi and Bluetooth, PACTOR, TAPR-2, Morse, but they simply provide the carrier.

Then data is imposed on the carrier by other layers of the OSI stack which provide the routing information, causing information to be communicated.

Here is an article that describes the OSI layers and what they mean

So no, I would not use that exact phrase in a research paper as you describe.

But you are very close.  You should be able to come up with a very succinct phrase that means what you intend and conforms to the OSI model.