I'm in a similar position, having a degree of esotropia (squint) which puts me out of Class 1 limits, even though I can better 6/6 with each eye individually.
The JAR limits are all published -
http://www.jaa.nl/jar/jar.html , and are broadly the same as the CAA's, although their are moves to ease the refractive correction limits which should (have?) take effect soon.
The rules state that you must have binocular (not neccesarily stereoscopic) vision, although I'm not sure of the exact definitions.
The JARs also allow the authority discretion on some of the standards where it can be shown that safety is not compromised in the particular environment.