"The application" in this case is just a blinking LED. I intend to use the ISR to read out a sensor and send the data with MySensors. But because I couldn't get the ISR to work, I reduced "the application" to an LED to keep this discussion focused on the real issue.
Yes, it always compiles, whether I include MySensors.h or not, and whether I use Arduino IDE or Atmel Studio.
It's just that the LED doesn't always blink. In fact, the LED only blinks if I compile with Atmel Studio and don't include MySensors.h.
I cannot use a serial monitor, because the custom node only has an ISP interface to program the MCU, there's no USB or anything like that.