Kelly,
To the extent I still remember my Aerospace Engineering classes from the last decade, the reason for commercial aircraft flying at high altitudes was that the air density was lower, thereby reducing drag, both around the body of the aircraft & in the engine. The other reason is that it takes less fuel to maintain the optimum fuel / air ratio for complete combustion. Also reduced variation in temperature in the lower levels of the stratosphere where these aircraft cruise, results in less turbulent air.
Other factors according to random people on the internet include
Dedicated flight corridors under an Air Traffic control who monitor the specified separation between aircraft
Sufficient glide distance to an alternate airport, if the aircraft loses 1 (or more) engines
Fly above the clouds to get around bad weather at lower altitudes
Minimize bug splatter on windshield & bird hits at higher altitudes
But realize that these benefits only apply to aircraft already cruising at that altitude. It takes considerable energy to rise to that altitude fighting against gravity through thicker air at lower altitudes.
The limits you mentioned if the aircraft approaches the limits of space (near vacuum), comes with efficiency losses due to
Much lower (approaching none) oxygen to maintain combustion hence thrust to maintain airflow over wings for lift & to propel the aircraft forward
More energy needed to overcome earth’s gravity to rise to that altitude, with reducing thrust from the reason above
More pressurization in the cabin to sustain human life & comfort without a space suit, adding more weight in cabin structure while getting less thrust
The issue of ozone depletion at the top of the Stratosphere (according to one of my professors)
Thanks,
Naveen Rajan