Pilots who hold a Part-FCL pilot licence may only fly under IFR in accordance with FCL.600:
FCL.600 IR — General
Except as provided in FCL.825, operations under IFR on an aeroplane, helicopter, airship or powered-lift aircraft shall only be conducted by holders of a PPL, CPL, MPL and ATPL with an IR appropriate to the category
of aircraft or when undergoing skill testing or dual instruction.
FCL.825 refers to the EIR.
So no. Under Part-FCL, a 'typical flight visual navigation from one aerodrome to another one when you are flying cruise flight about 3000ft' may NOT be logged as IFR unless the pilot is operating in accordance with FCL.600 or FCL.825 in accordance with IFR.