Once outliers are identified, they disappear as a problem. Admitted, you need to get rid of them for ordination to be most effective.
Re Monte-Carlo, ok. I should have referred to ‘MCAO’ as a permutation test rather than MC. Oh well, it’s in the system now.
Re CANOCO, it is up to you in PATN what variables you use in an ordination (SSH) – the intrinsic variables and what you may want to use for ‘environmental variables’ extrinsic variables. Standardizing variables is a serious issue in itself. Abundance data usually needs some transformation, but not standardization. Environmental data is the opposite.