At the moment, it doesn't look like the Clash Detection Algo works very well. The hard clash tolerance setting does not seem to work. Apparent works by 'shrinking' the elements... but some will fail.
There needs to a means of filtering out clashes by severity. 1-2mm clashes really should be sorted out.
A small survey of algos here. Naviswork seems to be able to provide clash distance info for every clash. But this is based on a ray intersection / minimum translation vector (MTVmethod) that I am not sure is very useful.
Maybe the geometric elements can be converted into a point cloud proxies and the 'clashing' point array evaluated to establish the severity or thinnest penetration distance.