Hello,

1) then they will necessarily have a different "Z" coordinate in jag3d, provided that "local elipsoidal system" is selected;

Yes, that is right. The local system has a direct link to a global (Earth fixed) frame and it is possible to project the points (using UTM, for instance). In your case, the defined local system is identical to the instrument/station frame. So, there is no need to reduce observations w.r.t. the frame.

2) then they will necessarily have almost the same "Z" coordinate in jag3d, provided that "local Cartesian system + Earth curvature" is selected.

If the network is quite small, the solution may be sufficient. The error depends on the network extent.

Kind regards
Micha