Okay, I can easily reproduce the issue -- here are some pictures.
https://imgur.com/a/qzizOv4The problem is basically duplicate phenotype shapekeys are added whenever a single phenotype value is adjusted. These duplicates warp the mesh, but it is solved by deleting the extras.
This particular character mesh is imported from MakeHuman not made from scratch in MPFB, not sure how relevant that is.
I have encountered something with the eyes as well -- morphing the area around the eyes works beautifully, but the actual eyeballs remain in the default position. This becomes a problem when the eye apertures are translated up, down, or to either side. This is probably some mistake I made, however, or something I need to compensate for within Unreal Engine.
Currently I have no morphs for alteration of the character height, or alteration of the length of limbs or any other 'length' body proportions, because that would cause problems within the game engine that I don't want to deal with at the moment. It would be nice, however I need to figure out how to maintain the proportion of the character mesh with the skeleton.
So, about the clothes. What I was going to do is export the base character mesh and use that as an 'avatar' in Marvelous Designer, which is what I use to create clothes. I haven't really used MakeClothes before and am not aware of its capabilities, but perhaps I need it. Obviously the clothes will have the same skeleton as the character, which I can do by exporting from MD, importing to blender, copy the skeleton and parent the clothes to it, and weight them, or something like that, I have done this before a few years ago.
I was thinking/hoping there was some way to copy the morph targets from the character mesh to the clothing, but now that I am working on it, I'm not so sure it's possible to do it that way. My understanding is shape keys / morph targets need the same vertex count (or topology), and obviously this is not the case with the clothes. Perhaps this is where MPFB clothing features comes in, but currently I have no idea how to integrate that with Marvelous Designer.
The eyelashes is a bit of a puzzle to me. the UV of the eyelashes seem to correspond to a spot in the upper-right corner of the body texture, which for me is empty. I do, however, have a separate eyelash texture from MakeHuman. They should be a separate material than the skin because they need transparency and do not need the features of my skin material, which has cumulative layers for dirt etc. However for my purposes eyelashes are a small concern -- that is a very small detail in the perspective of my project, where the camera through which the models are viewed is at a significant distance.
Actually, the character in MakeHuman does not have eyelashes. So that is why they are missing and only the helpers are left. Ah. I will have to redo some steps.
At some point I am going to have to add more bones. I have been using the community asset "UEngine" rig with default pose and that has worked for basic animation retargeting. But I would like some extra bones that aren't in the UEngine skeleton. I can probably add them myself but that will come later, right now I have to figure out how I am going to handle the clothing.
I initially tried to retarget the default MakeHuman skeleton because it has a nice supply of bones, but I had trouble. There is not a single "pelvis" bone but rather two, and this complicates retargeting. Also the character root was not on the ground etc. These I can fix myself with some more research.
I made a rudimentary editor utility in Unreal to copy all the morph targets from the base skeletal mesh into a data table, and also copy them from that list to a stuct attached to each instance of the mesh. This struct is then individual to each instance of the mesh and can be independently modified, then applied. I am still working out the best way to handle it all but this works so far, which is excellent!
Sorry if some of this is too off-topic
I should clarify that I am by no means an expert at rigging, character animation, or anything, so some of my issues may just be due to my own incompetence...