I have two cars on the company (and pay BiK on both), the second is very low mileage and on the face of it would not make sense, but the actual running costs exceed the BiK so I'm happy). Accountant approved it all (quite possibly because the second car is used for business mileage if the first car is unavailable for any reason; I do 30,000+ miles a year, so reasonable to say that a car is important! which may have something to do with it being justified in my case)
Bizarrely, the current regime makes it more beneficial to have a company car the
lower the business mileage (as a privately owned car can claim mileage allowance for business miles, while the BIK is unaffected by business miles). In the old days (20+years ago?), there used to be a lower rate for the BIK if you did a high business mileage (something like 10K miles/yr threshold, I can't remember), and there was a really punitive rate for having more than one company car for use by family members etc. The current scheme seems to assume that the BIK fully taxes the value of the car so there's no harm in you having as many as you want - which is probably true for ICEs, and is why many people gave up having company cars when the rules changed.
So far as I can see there's absolutely nothing that needs justifying. Nobody's claiming these cars are wholly and exclusively for business purposes (and if they were, the VAT would be reclaimable). Rather provision of personal use of a taxed, insured, serviced vehicle is part of employee renumeration. And it gets taxed as such, albeit that the rate will shortly be rather advantageous.
This is right. If the car were wholly used for business purposes, there would be no benefit and so no BIK tax to pay. So when you pay the BIK tax you are acknowledging that you get a personal benefit from having the car. For any ordinary benefit, the tax would be on the cost of providing the benefit, but for historic/policy reasons cars are treated specially and you pay tax on the 'notional' value of the benefit rather than the actual value. And it's very clear in the rules that insurance (and maintenance, but not accessories) are part of the benefit being valued.
Back on the subject topic (registration and insurance), I ran into one disadvantage of having the company as the registered keeper. I got a ticket from a speed camera; the car is registered in company name at an address where I get the post, so the ticket came to me. However, it said that as the car was in the company name I had to get the company secretary to declare who was driving on that day. In my case, the company secretary lives miles away; I was sorely tempted to just sign it myself, but the form had dire warnings about how doing that was an offence, so I had to post it to the company secretary, he sent it back to them and a new ticket came to me.
Likewise, insurance wasn't eased by registering it that way - if your company runs lots of company cars and has a multi-car policy then it's probably convenient to have them registered in company name, but for my case with one car and needing a new policy I found that nobody wanted to write a policy in the company name. Instead, the policy was in my name with the benefit assigned to the company.