Masking out (intrinsic) variables with low PCC correlation should reduce stress in ordinations. Ditto if you used the Kruskal-Wallis values from the box and whisker plots (but this is one step removed).
It is important however that the process should not be totally ‘mechanical’. Always seek to understand the trends in the ordination space and the identity of any groups from a classification. In both cases, examination of both intrinsic and extrinsic variables is important.