I have never used the tag in URDF, but my understanding from reading up is that it is not a way to specify an offset for joint values to account, but rather seems like the rising and falling attributes mark specific sensor-triggered positions to aid in the calibration process.

One way to modify this is directly on the motor, by using dynamixel wizard 2.0 and modifying the Homing Offset per motor. Have you tried that?

I believe using the Dynamixel Wizard for setup is very convenient when dealing with individual motors.
However, performing setup with the Dynamixel Wizard for a system or robot composed of multiple components is not ideal. This is because it requires a GUI to be prepared, and the calibration results must be reflected manually.

In the robot_calibration package, if the calibration only involves the joint's rotation direction, the calibration results can be applied by modifying the rising in the calibration tag without changing the origin in the URDF.
Based on this approach, I introduced offsets using rising.

Considering that an offset is applied to the trigger point (where the Dynamixel encoder reads 0), using rising does not seem unreasonable to me.