Is there a preferred way to export humanoids to MakeHuman so that I can put the mesh file into the babylon.js code and run it in a game?
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We do not support makeHuman as is, but you could certainly export to fbx and import in blender/3dsmax/maya where we do have exporters for both .babylon and gltf 
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The file based exports directly from MakeHuman are really not viable. Blender is the best, by far, way to go. For Blender 2.80, there is a the MH Plugin for Blender, which suck your meshes via socket right from your MakeHuman app into Blender, without dealing with any file format.
The current repo version for plugin is 0.61. I am going to add a small change in the day or so for dragging expressions, via socket, from MH directly to shapekeys, but probably not a concern for you.
You must be running 1.2.0 alpha 3 of MH to get the socket transfer to really work. http://www.makehumancommunity.org/wiki/Releases:120a3
If you export from Blender via glTF, meshes which have alpha like hair, eye lashes, eye browse, with not come across with out adjustment. You are on your own. I do not recognize the existence of glTF. I also have no clue about OBJ format.
For .BABYLON format, I do not use Blender’s UI for controlling Alpha Blend in their Settings section. I do not like that the default for Backface culling if false. Using all entries from custom properties for Babylon Exporter.
You make need to use Alpha Test & adjust the cutoff rather than just Alpha Blend in some situations. Here is an example using Alpha Blend which can illustrate the issue.
Here is an example I did today. In PBR, results are pretty good. Do not recommend the default skeleton though. Too many bones.
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