Actually the game uses both the Morph and the Obscure Vid.
The morph is used for the change in body size (skinny, muscular, or fat).
The Obscure vid hides sections of the player skin so clipping will not occur (and helps console's conserve memory).
Take a standard in game T-Shirt for example.
It will Obscure Vid most of the Character torso and upper shoulders skin, but will Morph to the appropriate shape/configuration of the character.
So a Fat Male Character in a T-Shirt gets the big gut, and everything that goes with that morph.
A Skinny Male Character in a T-Shirt will have a flat chest, abbs, skinny arms, etc
A Muscular Male Character in a T-Shirt will have a more defined chest, shoulders, upper arms, etc..
Some of the Morphs are not perfect either. You can see this in the Uncle Sam Costume.
If you max out the Male Character's Muscles there will be clipping in the shirt sleeves (back of the arm on the triceps).
This is due to the suit's morph setting not extending far enough in that area for the characters shape/configuration.
One of the best clothing items for a bad morph was the lace cloves in the Inauguration Station.
On a Female with the stock settings the gloves morph'd correctly to the arms. But if the character settings were set to 100% muscle, or 100% skinny. The cloves would morph in a very abnormal way and the top of the glove (which should have been on the forearm) would stretch towards the characters side/waist area.
That clothing item was removed from the store list in SR4, but is still in the customize_items.vpp_pc.
Back to the OP's question: How to extract the Player's Character from the game and export to a 3D render progam...
You are gonna have to wait for the SDK and then someone is going to have to figure out how to put the base character (built into the game) together with the modified player configuration (from the save file).
Now if you can figure out the data sent through the character gallery (the material sent to saintsrow.com for customized characters) you would have half of what you need. Cause that is pretty much the modified player shape/configuration along with a set of clothing.