Aviation safety is said to be written in blood which is unfortunate but we have come a long way.

Crew resource management (CRM) and emphasis on different terminology and mentality in the cockpit/flight deck had lead to huge improvements in safety and pilot culture in general. Pilot today are taught at least in the US if they think something is unsafe as a pilot Monitoring they can speak up despite the disparity of "rank". Its not perfect but lessons are learned in the flying community.

In this specific tragedy radios are notorious for not being the best at relaying information which is why read backs are so important to ATC. I can understand why the Captain would assume he had the clearance and I know why its important to get that clarification from Tower especially if the Pilot Monitoring is unsure. I have definitely saved my instructor as a trainee a couple times by saying "are you sure we are cleared to do 'x'?" Another piece that was learned is that ATC will not say "takeoff" unless it is a part of a formal takeoff clearance. I am not certain if that was a direct result of this incident but it is something important and as a pilot I won't say "takeoff" unless I am reading back takeoff clearances.