Apply scale under MU Hierachy works for model meshes and bashed colliders but not on anything wire frame.
Found this out while going through and removing vertices from the YnoT1300 mod. Box colliders, like airlocks and ladders, or axis like thrust transforms etc don't have the scale applied but rather get changed back to a scale of 1. Even if you don't highlight them before applying scale, if they are within the heirachy of a model mesh they will get affected. So if you do Apply Scale to your mesh so that it's current dimensions are considered a scale of 1, you will have to go and re-adjust any wireframe objects that are under it.
This is fixed in the newer .mu plugin used with Blender 3 onwards.