Hi, I was the same problem during many month. An electonic sound at every second and appears when i put the button on rec. I have try to find during long time, change different mic (zoom H6 etc) was same... Its was not a mic problem. I made a test with an another XT3, was same...
So i have try to reduce the audio gain to -20 in my XT3, and increase the gain to +20 on the external mic and the sound has disappeared.
It's very weird, but it worked. Why ? I dont know, i have send the question to fujifilm, I'm waiting for their answer