Different airlines have different SOPs. Airlines have different SOPs for different airplanes. So, an anonymous pilot in an anonymous Boeing airplane may well be following his SOP...
Some SOPs use switch positions as signals to the pilots that a specific clearance has been received (e.g., Taxi and Turnoff lights when Landing Clearance is received). It is not beyond comprehension that "All except landing lights" are turned on when clearance is received to Lineup and Wait, as in this quote from an anonymous SOP for an anonymous Boeing airplane:
Cleared onto departure runway | All except Landing
That SOP does NOT enter into a philosophical discussion of what the Controller may be thinking or doing when he gives a clearance. OTOH, is DOES tell the anonymous pilot that all such clearances must be acknowledged. Habit patterns (move the appropriate switches/buttons when clearance is acknowledged) are built for the general case, and some pilots are more bound to habit patterns without interruption...