Building Contractors have the means to claim their paid VAT back from HMRC and do in large quantities. I have seen HMRC come after small scaffolding contractors in the past for vat that was not paid to them by the main contractor. Hence the use of the Payment Application system instead of tax invoices to soften the sub-contractors tax liability in the event of non payment.
I havent yet fully read through the 2011 changes to the Construction Act to see if it affects the way PA's are viewed.
Also, Scottish law might give a different view to the claiming of vat.
Binthere, you are obviously more clued up than me on this and it has been a while since I checked for any changes but the payment application system is another thing I have never really understood. I have been asked loads of times to sign a self billing agreement but I like to keep it simple, price it build it and bill it, end off. They don't like me but eff em. You say it's to soften the sub contractors liability but when I signed up for vat I chose it not to become liable until payment is made as opposed to when the invoice is raised, does everyone not do that? Also, vat is national, Scottish law makes no difference.