So under the margin scheme:
You buy a car for £10000 hammer
Buyers fee (Gold) is £302
BCA assured charge £33
You total purchase price is then £10335 and this is what you put in your stock book as purchase price. Because this is taken into account when you work out your margin you don't lose out on the VAT. As Tony F pointed out the fees effectively reduce your margin. Where you WILL lose out is if you don't make a profit on that sale because there is no VAT due to offset against.
If the invoices (BCA storage a good example) have VAT separately displayed you just reclaim the VAT on the invoice and don't include it in your "stockbook" purchase price.
From the Gov.uk Margin Scheme for Second Hand cars. It gets EXTREMELY confusing when you read section 8.4. Basically they are saying that Buyers Premium and Indemnity fee are two different things although I loosely use the same wording for the same buyers fee at BCA :-)
8.3 Work out the purchase price of eligible vehicles bought at auction
Your purchase price will be the hammer price of the vehicle plus charges for services.
The invoice you get from the auctioneer will itemise, for each lot you have bought, the hammer price of the goods and any charges for services (for example, buyer’s premium). These charges must not show VAT separately.
This will be your purchase price for the purposes of the margin scheme or global accounting, and is the amount that you must show in your stock book. It should be clearly identified on the invoice you get from the auctioneer.
If the auctioneer bills you for any other services, and charges VAT on them separately, you can reclaim the VAT under the normal rules. You must not add those charges to your own margin scheme purchase price. To avoid confusion, you may want to ask the auctioneer to provide you with a separate invoice for such charges.
If you are in any doubt about what your margin scheme purchase price should be for a vehicle you have bought at auction, you should check with the auctioneer.
8.4 Indemnity fees
When you buy a vehicle at auction, you will usually be charged an indemnity fee. This is a charge which ensures that you will have compensation or indemnity if the vehicle you have bought is later found to have been stolen or to have finance outstanding on it.
You must not include the indemnity fee in your purchase price for margin scheme purposes.