On the second, yes, the VAT resource is capped. It is estimated that the UK gains an advantage from this capping (see the reason given in the EU document you quote), and the first "complication" in the calculation of the UK rebate is to allow for this by subtracting from the initial rebate amount a sum called the "UK advantage".
See this pdf for details.
In the pdf referred to, I would refer you to the table (page 11?) which shows the contributors to the cost of the UK rebate. France 27.37%, Italy 22.47%, Spain 13.99%, Germany 6.22%(?). Schroeder must have been one smart guy with a calculator.
I repeat. There is no logic to the system and looking for it only adds to the illogicalities. Special cases can be made for all Member States. The so-called "Rotterdam effect" in the case of The Netherlands, for instance.
One can look at it from the point of view of the game where one starts building a tower with childrens' blocks but the block marked "UK rebate mechanism" at the base is out of perpendicular. Every additional block is added in one direction or another try and keep the tower stable. But fall it will.
The only rough guiding principle that has emerged is that contributions should be related to wealth. "Each contributes according to capacity and receives according to need". The problem is that there is no agreement on what constitute legitimate needs e.g. the CAP. The results to date have been tailored to (a) trying to meet the GNI criterion and (ii) to the extent that this is not met, making those Member States insisting on an unbalanced view of needs (France for the CAP, Spain and Italy for continued cohesion spending) pick up the tab for the UK rebate.
The issues are political, not budgetary.
