Suzie, I hear what you are saying about it almost certainly being Marek's but you paid for a service and in my opinion (although I have only seen 2 pages of the report) but it sounds like your vet backs up my thoughts.... you have not received the service you paid for. What is the point of paying for a necropsy if they don't give you a definitive result. Is there a contact number on the report or email address? I would ask for clarification or at least whether testing for Marek's was conducted.
I believe there are some very experienced people here on BYC who have Marek's in their flock, perhaps a mild strain like the one I have and don't realise it. I so often read these people have typed, "it could be a sprain", when people report a lame bird with no obvious injury and state that they have had birds with a sprain that have got better in a couple of weeks when chicken's legs are incredibly tough. Or people suggest botulism, which is much rarer in chickens compared to Marek's. I'm also not entirely convinced about vitamin deficiency causing lameness or wry neck etc to any great extent. OK, possibly if a bird has been treated for extended periods with Corid perhaps, but I would bet that 90% of the time they are Marek's birds too. There is so much misunderstanding and misinformation about the disease, even with vets etc and the scientific community, perhaps because they only see the tip of the iceberg or worst case scenarios. and because there is such a huge variation in symptoms and range in severity from so mild you would not notice to fatal. So I would agree that it is probably in almost all flocks to some degree.
As regards disinfecting, Virkon S is the product that is supposed to be effective against the virus. Whilst I take basic precautions when I visit the feed store or other people's flocks or shows etc I don't go to the nth degree of disinfecting. My birds were free range at the time that they first came down with it and I was so busy dealing with the outbreak, I didn't even begin to think about the potential for spreading it..... I knew, so little about the disease in the early stages. Even if they were in a run though, making it so that wild birds cannot get it is nigh on impossible and it can still travel on the wind! In some respects they may be better free ranging as there is not a build up of infected material in a small area and they are less likely to be symptomatic and shedding the disease if they are happy ranging..... What would you do to all the material you muck out?..... Do you currently use it for compost and then spread it on your garden? If it goes to land fill there are usually birds picking through that. Do you incinerate, but there will always be material that blows away during that process. I think you have to just accept that it is pretty much everywhere but take steps to prevent direct exposure to other birds/flocks by not selling or swapping, changing clothes and shoes when visiting other flocks etc. I would probably give the car a good vacuum. That is the best I can suggest.