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TL;DR In order to remove base_footprint you need to modify and reflash OpenCR code.
Long explanation:
You still seeing base_footprint because OpenCR is publishing transformation between odom and base_footprint. That's why even if you will remove the frame from URDF you are still seeing base_footprint frame.
I guess that right now base_footprint frame (with parent odom) is disconnected from your TF tree, as you removed base_footprint from your URDF. It happens because there is no connection between base_footprint that is published by OpenCR and base_link from your URDF.
Here is the code for TB3 Burger: https://github.com/ROBOTIS-GIT/OpenCR/tree/master/arduino/opencr_arduino/opencr/libraries/turtlebot3/examples/turtlebot3_burger/turtlebot3_core
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