advantages and disadvantages of using a microcontroller vs dedicated switching controller for a switching power supply?
Well as you mentioned, the microcontroller has a dominant advantage of ease of use (because of the ability to program it) when you want it to behave as switches for particular components for your machine.

The main advantage of having a microcontroller is the ability to make things conditional and intelligent based on how the user perceives data to be sufficient for what they're trying to accomplish. With a microcontroller, you are able to predict and perform behavior instead of relying on the electronic switch to do it for you and thus you could really prevent error within the machine.

Some disadvantages I can think of is cost or programming error. The cost of a microcontroller can get pretty expensive. You can probably make your own circuit for a much cheaper price because those Arduino/Beaglebone/Raspberry Pi modules can get pricey. Programming can also be disadvantage. What if you accidentally messed up on your code and then you distribute the product to your client? Programming can also take longer to perform than circuit analysis.