When you buy goods from within the EU, you have to pay the VAT at the rate that is applicable to the country the goods are sent from.
Now, with ebay trade things get a bit trickier. Let me use my own experience and business as an example.
I am registered for flat rate VAT. That means that I hand over to HMRC VAT on any sales I make to any EU country. So anyone flashing their VAT registration number in front of my nose still won't get a VAT exempt sale. And why not you ask. Well, that's because the VAT man doesn't care if I sold the goods without VAT. Under the flat rate VAT rules I am still liable for the VAT. It is quite possible the Polish seller is in the same predicament at his end.
Now coming to eBay. They charge the seller a fee based on the final selling price plus postage. And that is the price that will appear on the Paypal invoice. Any amendments to that amount has to be done by the seller within eBay before it is sent to you for payment. He cannot amend it from within Paypal. Neither can he charge you a different amount in Paypal compared to the final price in eBay. If he tries to circumvent that, the seller could quickly get a note from both eBay and Paypal stating that his days with them are numbered. So you won't find many sellers who are sympathetic to your plight if they are aware of this eBay/ Paypal sword of Damocles.
For VAT free purchases within the EU it is best that you confirm beforehand with the seller that he can do a VAT free sale. If you first buy the goods on eBay and then confront the seller with a VAT registration number afterwards, I don't expect you to get away with not paying the VAT. Sellers would rather refund you the payment.
You can reclaim the difference in the VAT if the goods are sold on with VAT added. But if the purchase was not for resale purposes then you'll have to take a hit on the Polish rate of VAT.