I believe the reason Mark recommends cutting out high-PUFA oils is that the total amount of PUFA you get from them would typically be greater than the amount you get from eating the whole nut. Also, the PUFA in the oil is more fragile and easily oxidized than the fat stored in the nut. The extraction process may contribute to oxidation (if it involves high heat, solvents, etc).
I limit my intake of all nuts since they are all pretty high in PUFA. The omega-3 content is kind of a moot point since the body converts the plant-form of omega 3 (ALA: Alpha linoleic acid) into the active forms (EPA and DHA) pretty inefficiently (like ~8% or less if I recall correctly).