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My last option is to try and create a node that subscribes and republishes the data on the topic with my given covariance values, but seems like an annoying workaround, and i was wondering if anyone had a clue on how to set these values someplace else?

I agree. This workaround is not the best way to acheive this. Unfortunately this feature has not yet implemented. Please submit an issue about this on ardone_autonomy's github repository so we can start the technical discussion there.