Greetings,
When I first logged on I only saw your first reply and was to start answering best I could lol! Every post after was another question, then you seem to have solved all of your problems! Kudos!! Anyway I still will address a few questions here in effort to continue your journey in relative peace ;0
Bones-never used bones for makeclothes at all, but they are ok to add makehuman side and should not affect the clothing makehuman side at all. Proxy likely may...
Pose is ok, T pose model is fine for porting, I use the T pose for things like fringes on arms all the time! Topology however is something that can cause issues without a lot of work.
Im not sure what you mean about using mesh in other program? But the base mesh is a mix of female and male bodies /unisex. Therefore it is not suitable for most male or female instances It is not ideal for porting in lots of cases either.
Makeskin works quite well, have not worked with it much except for reverse engineering during my post process-but it is quite viable. Materials can also be made on the material tab in makehuman with existing textures. As long as you export the uv layout blender side you can make a material texture for this in gimp/ps etc also.
Pokethroughs or clipping as its called in the industry is common yes, this can be helped using delete group or z depth, play with it a lil but know some is normal and can be fixed in other programs in post process.
Sidenote: first textured successfully ported clothes in makehuman look great! Congrats
Elv
She who knows in repose with prose...