I just tested this out quickly, and I am happy to confirm that it works:
So, to summarize, the working process for me was:
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Create and download a Metahuman.
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Open the maya source file included in the bridge directory.
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Export to Zbrush (or whatever 3d package you want to use) and make your changes.
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Bring the changed mesh back into Maya, add it as a blendshape.
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Fix the bone heirarchy of the skeleton in Maya (face starts at Spine_04 in Maya, but it needs to start at root).
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Export the head with all the morph targets included from Maya. Import it into UE.
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Apply materials, make sure that the Metahuman animation blueprint, Control rig, and other animation assets match the default Metahuman setup (compare to an existing MH skeletal mesh to confirm).
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Import the DNA file with the method described by the post above. Drag it into the editor from the SourceAssets folder, select your newly imported mesh in the dialog that appears.
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Your changed Metahuman face should now work properly with the Control rig! You will have to either set your blend shapes to turn on at runtime (through a metahuman or level blueprint), or you can use a plug-in from the Marketplace to bake the morph targets onto the mesh while preserving all the face deformation morphs needed by the rig.
Thanks again to MAkiNA - crazy to think the solution was sitting in front of me that whole time and that it was so simple…