Instruments, by the S88 standard, are a form of control module (CM) designed to handle process inputs such as transmitters and discrete limit or push button inputs. Instruments do not make up the EM route. If the input is used to verify the route such as a flow plate prox. sensor then it should be configured as a CM. Also, inputs used as feedback for control outputs should be configured as an input to that control module. Any input may be configured as an instrument even if it is also part of a CM.
For Example: a control valve analog position or limit feedback would be part of the CM and Motor current on a VFD would be part of the VFD CM. However, Flow feedback for a PID flow controller would not be part of the PID CM because the PID CM is a wrapper that wraps a CV-CM and a PV-Instrument. If a complex CM is created that is designed around hardware that uses flow as feedback then the flow would be part of that CM; however, it may also be configured as an instrument as well.
Instruments may be analog, digital or both.