Hi Edward,
Currently you can only assign a constant initial thickness in GPlates. We plan to implement the importing of an initial thickness grid as you noted.
However in pyGPlates you can now do this and it will be available in the next release (after GPlates 2.3 is released, which is soon). You would still need to provide the point locations and initial thicknesses yourself (eg, sample a thickness grd/nc grid). Although before the release we will expose the ability to generate uniformly spaced points on the globe (ie, not just uniform lat/lon) inside a chosen deforming region (ie, polygon boundary). Which means you would just need to take those points and sample the initial thickness grid yourself.
It sounds like a problem with feature IDs of some sort. Have a look at this post, but that might not be the answer since you’re not saving and reloading. Even though the mesh does not appear, can you save the mesh to GPML and send to me along with the file(s) containing the features it references (ie, the ones you added to the mesh)?
You can add a regular feature (reconstructed by its plate ID) or reconstructed by half stage rotation (eg, mid-ocean ridge). But you cannot add a VirtualGeomagneticPole, SmallCircle, motion path or flowline.