MATS pt 3 - I hear what you are syaing - and I guess it depends on a particular unit and its intricacies.
i.e. We don't have the luxury of vertical separation when the MSA is 2300ft and the base is 2500ft.
Laterally things don't get better - and at the LTMA approach units traffic outside CAS even if IFR is low on the priority as detailed in the pt2.
You are right - we aim for standard sep'n, but 2nm and 700ft is better than nothing if you are busy and have no airspace to play with!!
Finally, as you stated above, the MATS pt 1 says
Standard vertical or horizontal separation shall be provided, unless otherwise specified
So, if we said something along the lines of "Standard separation will not be achieved due to blah blah blah" then that would cover you - would it not? I think if you did everything reasonable that you could you would be in a better position.