Heat sinks on individual components are calculated for maximum allowed junction temperature in a certain ambient temperature. If the ambient is higher than a value used in calculations, the die will potentially run hotter than intended. The safety margin used in the calculations is a lot wider than few degrees ambient temperature rise, though. In my case, as the fan speed is temperature controlled the system will settle on some equilibrium point where the fan runs at sufficient speed to prevent further ambient temperature rise. As long as this point is reached at lower than maximum fan speed, the temperature is kept under control. If this point would seem too high, then changing the temperature/speed relationship is just a microcontroller firmware change. After running the scope for many hours and looking at how long it takes for the temperature to even get up to the point where fan starts I don't think the mod will cause any problems.