Nice question, thank you! I agree with @sandris that distribution of lap times matters, but would like to emphasize that causal aspects of the question need to be addressed. My guess is that F1 wants to avoid a boring situation where the same team or driver dominates the sport year after year, and that they especially hope to introduce the (revenue-generating!) excitement of a real possibility that 'hot' new drivers can suddenly arise in the sport.
That is, my guess is that there is some hope to disrupt excessively stable rankings of teams/drivers. (Consider the analogy with raising the temperature in simulated annealing.) The question then becomes, what are the causal factors at work, and how are they distributed across the population of drivers/teams so as to create persistent advantage for current incumbents. (Consider the analogous question of levying high inheritance taxes to 'level the playing field' in society at large.)
Suppose incumbent teams are maintaining incumbency by a conservative strategy heavily dependent on driver experience, that emphasizes low variance in lap times at the expense of mean lap time. Suppose that by contrast the up-and-coming teams with (say) younger drivers, necessarily adopt a more aggressive (high-risk) strategy with larger variance, but that this involves some spectacular driving that sometimes 'hits it just right' and achieves a stunning lap time. Abstracting away from safety concerns, F1 would clearly like to see some such 'underdogs' in the race. In this causal scenario, it would seem that a best-of-n-laps policy (large $n$) would help give the upstarts a boost -- assuming that the experienced drivers are 'set in their ways', and so couldn't readily adapt their style to the new policy.
Suppose, on the other hand, that engine failure is an uncontrollable event with the same probability across all teams, and that the current rankings correctly reflect genuine gradation in driver/team quality across many other factors. In this case, the bad luck of an engine failure promises to be the lone 'leveling factor' that F1 could exploit to achieve greater equality of opportunity--at least without heavy-handed ranking manipulations that destroy the appearance of 'competition'. In this case, a policy that heavily penalizes engine failures (which are the only factor in this scenario not operating relatively in favor of the incumbents) promises to promote instability in rankings. In this case, the best-of-n policy mentioned above would be exactly the wrong policy to pursue.