First question is export settings.
For 3dsMax using Game Zombie's DMX tools, I wrote a program available on my website called DMXProc. You write out your QC with all of the $model and $bodygroup lines out, then throw the QC at DMXProc, and it will process the DMX files and rip out the duplicate flex sliders. End result is a single set of flexes that work for all of the bodygroups.
For Blender, the way I understand it is you have to manually turn on Advanced Options and turn off exporting sliders for everything except the first bodygroup that has your flexes. Note that this causes problems if your bodygroups have different flexes. It sounds like a really clunky solution to me, but I don't think the Blender DMX tools can export as ASCII model 18, which is the DMX format that DMXProc is built for. So you'll have to figure that out yourself.
Second question requires a little bit of mesh and material hoo-hah.
For brevity, we are going to refer to four things. You start with these two:
TRANSPARENT MESH is the normal mesh you want to make transparent. TRANSPARENT MATERIAL is the VMT that is applied to it.
What you do now is you make a duplicate of TRANSPARENT MESH. Refer to this duplicate as ALPHA MESH. Apply a material to it referred to as ALPHA MATERIAL.
Flip all of the normals of ALPHA MESH, and then export both TRANSPARENT MESH and ALPHA MESH as a single model or bodygroup. They will be perfectly on top of each other, normals facing opposite directions, with two different materials on them.
Now, make sure that TRANSPARENT MATERIAL and ALPHA MATERIAL have identical material settings. Same basetexture, same phong, etc. They must also both have the parameter $ambientocclusion 0.
These following parameters are exclusive, meaning that while one material has it, the other does not.
TRANSPARENT MATERIAL needs to have the following settings: $translucent 1 and $nocull 0
ALPHA MATERIAL needs to have the following settings: $alphatest 1 and $nocull 1
If you get the meshes, normals, and materials all correct, then your transparent material should work correctly.