@ thandermax
As correctly mentioned by rajelectronic VAT and Form 50 are separate things. Also if you are selling something to a buyer in WB, its not compulsory to register yourself to WB government as u stated. VAT can be paid anywhere. but for getting in the product inside a state there are some regulations and taxes.
For eg- Octroi in Nagpur.
But I see that you are still linking them together.
VAT receipt/bill has to accompany the FORM 50.
Also as you said about VAT registration status of sellers, there are some guidelines regarding it which are available for reference in different state Gazzetes.
Most of eBay sellers have a low turn over which does not falls under Compulsory Vat registration. wherin big seller with offline shop as well are having registrations done. (Also registration has to be done within 6 months of starting business/crossing threshold, but it is mandatory to maintain record of all sales which in eBay's case is done by the eBay server as the files which are available for download's to sellers)
So to sum up the it's not the issue of VAT for shipping to WB, but Form 50 which has to be filled by buyer's and dispatched to seller to be accompanied with the parcel.
There is little eBay or seller's can do about it.