@jonathankampia, the way that voxl-microdds-agent works is that it wraps around the XRCE microdds agent binary from e-prosima, and bridges the px4 microdds topics to the DDS global data space (e.g. ROS2 topics).
The voxl-microdds-agent runs irrespective of any serialized message definitions, so it is just the transport. Probably not the issue, but if you still feel strongly that the agent is the issue, there are ways to test that.
Most likely, the mismatch is between px4_msgs and the voxl-px4 version. In that case serialized message definitions DO matter, and the mismatch could cause issues, but usually this is caught when the dds agent service runs (it will report errors you can view via systemctl status).
What sdk version are you using on the voxl2? You could checkout the submodule px4_msgs version that voxl-mpa-to-ros2 uses.
It would be difficult to troubleshoot without the actual offboard code to test, maybe post a snippet of your code?
For an offboard example using trajectory setpoints, you can also try this one which has been referenced a lot in the PX4 community