The combination of altitude and cruise speed that an aircraft is capable of attaining is a function of how heavy the aircraft is (how much fuel, cargo, and passengers) as well as the atmospheric conditions (temperature, pressure altitude, etc.).
The engines are no more susceptible to flame out at higher altitudes because the fuel scheduling is electronic and extremely reliable. It also doesn't put additional stress on the airplane to go higher, it's just that an airplane will eventually reach an absolute ceiling in which it simply can't fly any higher. To fly at a maximum altitude, the pilots will determine the highest altitude that they can currently fly (or the altitude in which a minimum rate of climb, such as 500'/minute, can be attained) based on their weight and the atmospheric conditions. Usually, they don't choose the absolute maximum altitude but rather, the maximum altitude that they can attain a specfic climb rate. They will then choose the next lowest altitude as required by ATC (in other words, ATC isn't going to let you fly at 38,418 feet, however, if going westbound, they will let you fly at 38,000 feet, so this is the next lowest altitude compatible with ATC). Pilots will analyze their current conditions before requesting a climb. Current conditions are constantly changing because the airplane loses weight as it flies along and burns fuel and the temperature can vary substantially over a defined geographic area. Aircraft pressurization systems are designed to provide a cabin differential pressure that reaches a maximum limit. Once the maximum differential pressure is reached then as the plane climbs higher and higher the air pressure inside the cabin will also continue to climb at the differential rate. But that doesn't hurt the airframe.
There have been times when I have been flying along at high altitude and suddenly the air will warm up a little. The throttles can be advanced up to a point, but if greater thrust is required than what the engines are capable of producing, the airplane will slow down. If the airplane slows down too much, a descent to a lower altitude may be necessary. If you stay in the same pocket of warm air for an extended period of time then you will continue burning down fuel and eventually, the airplane will speed back up to its original speed. Either that or again, you can decrease altitude, or find a colder air (which really isn't practical).
As a pilot, the highest I have flown is 43,000 feet.
C-5 Galaxy Instructor Pilot, licensed Airline Transport Pilot