With the registration of my two Troll scooters, the first forms were sent back by DVLC.  Two issues.
  
1. No HMRC NOVA records.  I had to fill in forms for HMRC to explain when the vehicles came into the country.  Mainly to do with VAT I think.  Hard copy with covering letter to HRMC as internet versions did not cover vehicles already in the UK.
2. I said that I wanted to register the scooters before restoration - they said register them once they are restored.
I wrote back to DVLC Swansea explaining that both vehicles were made before VAT was introduced and that both had MOT's and were road worthy.
Within a week I had registration docs and tax discs.  A few days later HMRC gave me the NOVA reference number.  So did DVLC proceed without the NOVA customs number?
It may not be so much 'whose desk it lands on' .
It may be that the first attempt with DVLC is dealt with by rejection on whatever grounds look relevant - easy.  The second attempt is looked at more closely and is more likely to proceed - easier to accept rather than argue against?