Can I use my own Microphone with Metronaut?

Yes!

Metronaut automatically chooses the last microphone you have connected to your device or the best one for its performance.

You can verify or change the microphone from any music score by going to Tools, and then  choosing Audio and in Microphone Settings section tap on Source (see screenshot).

Note that by explicitly choosing a different microphone than the one automatically selected, it will be remembered and used in every session (if the microphone exists) on the same device.