In which coordinate reference system are they stored?
It could be that they can only be shown in the radar image after its geocoding. Additionally, as far as I know, the GCPs will not affect the “phase to elevation” progress.
What you can do is to geocode the InSAR elevations, then import the GCPs and remove trends or over-estimations by a linear regression (I discussed this in another topic: here). Do you think that would help?
A first step is to plot the heights from the InSAR DEM against the heights of the GCO points. This will show you if you can increase the quality of the DEM by a mathematical expression to bring the values into a more reasonable range.