The OE fan/hintsink works fine as far as controlling temps to AMD's max specs other than some possible noise issues for some folks. Aftermarket HSFs can lower noise and temp but they are not a requirement unless your ambient room temp is 90+ F all the time in which case you might want to try air-conditioning to help your body and your PC.
If you have a small PC case or poor case airflow this will definitely cause high APU/CPU/GPU temps and should be corrected for proper component life.
As far as PC fan speeds it's a given that if you are NOT running them at the proper speed of course the APU/CPU/GPU can all run hotter than specified or desired. Newer BIOS tend to set the fan speeds at less than 100% to reduce noise but as a PC builder you need to make the correct BIOS settings for your PC to cool and function properly and as you desire.
In the past CPU fans always ran at 100% and this was fine for most people but it's nice to be able to adjust them via the BIOS or with applets like "Speedfan" so you get enough cooling with minimal noise for sensitive ears.
Building a reliable PC involves more than just assembling the parts. You need to be able to configure all of the BIOS settings appropriately. This can be quite involved and frustrating as it can require a lot of trial and error with stress testing. It is however often the only means to get a 100% reliable PC.