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From what you described, the issue is that you are feeding the wrong odometry topic to navsat_transform_node. Here's how it should look:
EKF 1 (odom frame)
Inputs: /imu/data, /odom
Outputs: /odometry/filtered, odom->base_link transform
EKF 2 (map frame)
Inputs: /imu/data, /odom, /odometry/gps
Outputs: odometry/filtered_gps, map->odom transform
navsat_transform_node
Inputs: /imu/data/gps, /ublox_gps_rover/fix, odometry/filtered_gps <-- You need this
Outputs: /odometry/gps
Your issue (or at least one issue that I see) is that you are missing a remap in your navsat_transform_node launch:
<remap from="/odometry/filtered" to="/odometry/filtered_gps" />
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