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If a GM rules that the barrier doesn't block the attack then it isn't 'cover'.
Just because there is something between attacker and target does not mean that thing automatically grants cover. Otherwise, air or water would provide cover.
If a material has hp/hardness in some book (just to cover splat books like Ult Equip etc), it is cover (by examples given - walls with large holes and the like). If it is a physical obstruction between you and the target, it is cover (as evidenced by water providing cover). It is pretty well defined in that way. Cover may be abstract, but it isn't that abstract.
If a GM wants to house rule / hand wave otherwise, that is what they are doing. That doesn't change what the rules actually state.