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I sounded confused, but I feel much better now :) To answer my question, scanmatcher frame is there for debugging purpose - it's what map-based localization think base_link is, and realized as tf transform between map and odom frames.

The iRobot driver I used has a driver.py wrapper that publish odometry but also a tf message between odom to base_link. I had to comment out the tf message part if I wish to fuse wheel/imu/vo odometry using robot_localization or similar filters.