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Is this simply because ~zero_altitude only affects the Odometry messages on /odometry/gps & not the NavSatFix messages on /gps/filtered?

In my understanding, Yes, that's true!

From the package documentation and precisely the part talking about the navsat_transform node

~zero_altitude

If this is true, the nav_msgs/Odometry message produced by this node has its pose Z value set to 0.

Regarding the ~two_d_mode parameter,

It should be set to true if your robot is moving on a planar environment or to ignore the subtle effects of variations in the ground plane that might be reported from IMUs if it's not.

/gps/filtered is an optional topic where filtered NavSatFix messages generated from the output of the gps odometry are published in case this data is needed (sort of a reverse navsat transform).

A NavSatFix message with 0 altitude does not make sense, if we don't need altitude we can simply ignore it.