I have seen engineers slap Teensies on a PCB and call it a day, so it’s definitely normal. It’s faster than having to route your MCU, USB, debugger, etc. manually, so there isn’t really a drawback as long as it physically fits there.
Common misconception. A handful of capacitors, SPI NOR flash, an inductor, and a crystal is way easier to place and route than a restrictive module that completely disables your ability to use SWD/JTAG on an otherwise excellent MCU.