I have been looking for a "Taiwan" coo vader for a while and I keep seeing vaders that are AFA graded with a TW or even Taiwan on the label. My question is does AFA put this on the "Made in Taiwan" coo also or are these the "Taiwan" only coo?

Also if they put it on both is there anything that you can use to determine which coo it is since you can no longer see the coo on these imprisoned vaders?

Not sure about the AFA question, but M4K3R1 has a nice limelight showing some of the differences between several 'TAIWAN' variants which may help identify any differences, you can check it out here
 
Hope this helps

Both MITW and TW Vaders are almost impossible to tell apart,
both of these CoO share the same features, and the only way to tell them apart is the CoO stamp on the back of the leg.
I have an AFA TW only Vader with a grading summary from AFA, that says it is a TW only CoO.
With out this AFA document i would consider it to be a MITW CoO.
The AFA label on the case is exactlly the same as a MITW AFA graded Vader, both the MITW and TW will have TW on the AFA label.
A while back, i wanted to try my luck, and bought a reasonablly priced Vader TW AFA80 on the label, from ebay but without the AFA document saying it was a TW only.
When i received it, i cracked the case open, the figure had a MITW CoO.
A graded TW only CoO Vader, should have the afa document to accompany it.
IMO.

That is disappointing. You would think AFA would make some sort of distinction on the label, especially considering how rare the Taiwan only variant is and considering that once they are entombed you can never see the coo marking. Just another reason not to AFA certain things.

a smooth no CoO or scar CoO is just '--' so I don't expect much from AFA re loose variant labels.