Websites can be designed so as to be useable by people with disabilities. Pages which can be used by the disabled are refered to as "accessible". These are the World Wide Web Consortium's Web Accessibility Guidelines, which define three diferent levels of accessibility (Triple-A being the most accessible), and the US government's Section 508 Guidelines.
This site has been designed according to the Triple-A guidelines, and is also Section 508 compliant.
No automated tools are 100% foolproof. In particular, some tools will give false negatives. In the case of mantranet, this happens where tools are incapable of recognising that relative and absolute links are actually pointing at the same resource. (It is one of the accessibility rules that the same link text cannot point at different resources).
In fact, there is only one version of each page. The different views are just that - different ways of looking at the same material. The reason we decided to have two different views is that the Triple-A rules are so restrictive. There is no point having a site which is wonderfully accessible, but very few people want to use because it is so unattractive.
No. We have departed from the accessibility rules when in the standard view in order to make the pages more user-friendly, and to make the best use of screen "real-estate". We have also occasionally had to depart from the accessibility rules when in the standard view in order to make a page work properly in the real world. This is because there is a gulf between the rules that browsers should follow, and the actual implementation of those rules in the browsers, as well as the existence of many small bugs in the various commonly used browsers.
Where we have departed from the Accessibility rules in the standard view, however, we have done so in only minor (and technical) ways. For example, on one page we have broken a minor rule of XHTML syntax in order to get around a bug in Internet Explorer. As pages must conform to the official syntax as a precondition of being considered accessible, such a page could not technically be classed as accessible. It is ironic but true, that for the vast majority of our users, if we were to conform fully to the accessibility rules in the standard view, we would actually make the site LESS accessible.