I've deployed my fair share of both and SBCs are still a very widely useful middle ground. Being able to use existing Linux tools instead of limited or nonexistent embedded libraries is a huge benefit. Most things to do with sound or video, for example, are totally infeasible with microcontrollers. A mini PC is noticably bigger and you need to add a microcontroller over USB if you need absolutely any real world interaction (even something as simple as sensing ambient light to adjust brightness).

My new favourite tool for these situations is the Radxa X4, which is the exact dimensions of a RPi, but with an Intel x86 CPU and an onboard microcontroller to drive GPIOs.