currently JSIAdvTransparentPods is using the old JSITransparentPod way of showing the IVAs/transparentpods in the Editor (VAB/SPH). Initial attempts to do it the new way (using an additional camera and depth mask shader meshes) resulted in some bizarre results.
This is because there appears to be Offset cameras? in the part selector/whilst transfering a part from the part list onto the craft/vessel being built. Which results in IVAs being offset.
Strange camera effects with relation to the layers - seems the Ground Crew kerbals and trucks passing by the VAB hanger doors, etc are on the IVA layer?? or suchlike, as testing resulted in duplicates/offsets of these gameobjects as well.
It may be that this is not possible to overcome? But requires investigation.