So I mentioned in the first Face Effect tutorial that I didn't quite understand what the LODx collections do but it likely had something to do with the geometry of your face as well.
Well, first, LOD1-LOD3 generally don't have anything in, but maybe they do for some of you. I only had data in LOD0 and so, for interest's sake I deleted the data in this collection. What happens?
I was expecting a crash. Instead I got this. It's an interesting twist because if one saves the game, then examines this latest save you will find this data is rebuilt. Not exactly the same either, but the same number of entries (more than ME2).
This suggests that the key differences between a YAML (or indeed any face code generated Shep) and those sitting somewhere inbetween (ME1 imports, ME2 new game+ imports) are dictated by subtle nuances in this LOD collection.
Now, previously I demonstrated copying over about 100 variables in total. The LOD0 collection by itself in ME2 is 2232 (0-2231). ME3 has 2390 (0-2389). I attempted to get a macro going to copy this but unfortunately I didn't have much luck with the automation. Regardless, this might be the secret to why your Shep isn't looking the same, along with issues in the MorphFeatures and OffsetBones collections.
In fact, this effect can be noticed further by deleting the MorphFeatures and OffsetBones collections as well.