They know "approximately" how long routes take from past experience, and guess their speed from the theoretical distance traveled.
You can't actually expect people to believe this complete and utter rubbish surely? I know that you don't believe it, so apart from amusement value why pursue it when it has been shown to be rubbish over and over again.
Any pilot flying a long distance route would have to know the exact distance to fly and would also have to know the speed to fly to maximise the fuel consumption of the aircraft. Any miscalculation due to 'Guessing' anything could and probably would have disasterous results putting a large number of peoples lives at risk including the pilot's own life. The balance between all up weight, distance to fly, speed to fly and fuel load is absolutely critical and anybody guessing any part of it would be very stupid. The speeds, payloads and fuel vary for every type of aircraft, every flight and every route, These variations are due to passenger numbers, baggage weight, aircraft performance, prevailing weather and wind conditions and several other lesser factors. To suggest that any part of it is based on unknown factors is either very ignorant or very argumentative at least.
There are a number of ways that accurate aircraft speed is ascertained and this has been covered very fully in other threads as you well know. Don't bother to reply with comments that aircraft often arrive late because they guessed wrong. Aircraft do however take longer occasionally than expected due to changes to headwind strengths, which are relayed to the pilot and also seen by the pilot and the inflight computer systems as a direct read out sourced from ground radar speed, airspeed inertial guidance instruments and gps, all of which work together to give accurate speed and position indications. Aircraft are also delayed by the need to divert around large storms. Ground stations will also be able to keep an accurate track on any aircraft position and speed from their own radar and data information transmitted from the aircraft by its satellite relay systems and transponder. If you would like to see information regularly updated for all to view, just go to any one of a number of online aircraft tracking programmes which will give you constant updates on aircraft positions, speed, height arrival times etc. All very interesting and a valuable tool for any flat earther wanting to find distances and speeds superimposed over an accurate global map. I've even used a tracking programme to follow a friends aircraft as he flew up to a local airfield to give me a flight.
Roger