In a case reported here, the taxpayer won the right to recover input tax on company cars. http://financeandtax.decisions.tribunals.gov.uk/judgmentfiles/j11273/TC07313.pdf
The taxpayer succeeded in arguing that the vehicles were not available for private use
- the drivers had comparable cars of their own;
- their contracts of employment explicity prohibited private use of company vehicles
- the keys were kept in a safe to which only the director had access
- there were mileage records showing that substantially all of the usage could be accounted for by business trips.
As this was a VAT appeal, benefit in kind charge wasn't within scope but I think the same rationale would carry the day.
So there you have it. Anyone that wants to recover input tax and avoid bik charge just has to make sure that the cars really really aren't available for private use.