We dealt with a similar and at the same time slightly different issue raising case earlier this year. A stray cat which was obviously just lost but which had a french chip. We had accepted the cat into our care so we had accepted responsibility for it. As soon as the chip problem was discovered, all kinds of nonsense started.
We tried desperately to trace an owner using all kinds of methods but nothing brought us forward.
The problem you are going to find, and expect are already finding, is that one will want to know. They will all point to each other and pass the buck. DEFRA really couldn't care less, nor could RCVS or any other authority we spoke to. CP guidelines state any cat whose imigration status is unclear for any reason needs to be quarentined. End of story. That's exactly what they will tell you when/if you call them.
The puss in our case HAD to go into quarentine for six months and HQ kindly covered the bill as it would have sunk our small branch. As far as I know, puss finished its period in a DEFRA approved quarentine cattery and then went on to the National Cat Centre and get rehomed.
The sad thing is that it very probably was imported legally and properly but we had no way of proving it.
In your case, I'm surprised Trading Standards got involved and I think secretly they are already regretting it deeply.
The fact remains your kitten was vaccinated with a product whose origins are outside this country (either obtained legally or illegally), it was not administered by a professional prepared to vouch for fact it was done here in the UK, and no one has any way at all of proving the kitten itself did not also come from outside the country. The breeder's word for it is not acceptable proof in any legal way. Sorry, I really don't see how you can avoid going down the quarentine route now that TS have made it 'official'.
