"As I understand it (from a brief conversation with my accountant) you are having to submit a lot more than boxes 1-9. He said all transactions involving a VAT element will need submission so presumably they can match the claimed refunds for one business against the sales for the other."
I suspect that was sort of what they were originally thinking - and when it was still at the planning stages some time back, I read stuff (on HMRC's site, I think) that suggested that during the submission process, the server could request more background data from the submission client. i.e. they could interrogate your software for the full data.
However, even that's been scaled right back - to the extent some people have told me I was imagining it; I'm sure I wasn't. If you look at the API (I've linked to it in comments on El Reg before, and someone else has done so further upthread) it does indicate only the main VAT return boxes.
There is supposedly a requirement that the figures be built up digitally (because that was supposed to be the point) - but AFAICS you could still keep manual records, and just key the VAT return figures into something that will then submit them, and they would be none the wiser at this stage*. It's all a big exercise in wasting lots of money.
* Things might change in future, of course.