It seems the tracker has to go in certain orientation to match ok with the live video. In my case im using a logitech c920 with a vive tracker, and a 3d printed adapter to locate the tracker just above the camera with LIV and never had any weird issue. In the Unreal mr plugin case, that tracker has to go rotated 90 degrees in Z (weird since its not correct if you check vive´s tracker documentation).
Since the sav file generated by the calibration tool, isnt editable as plain text. Now i have to redo all the calibration process just because i needed to adjust the tracker rotation axis. I know this tool is still in wip, but would help a lot if documentation is more clear about all this stuff.