Ultimately, this comes down to whether one interprets 'functions like [X]' as letting a spell count as that thing or not. The rules are unclear on that topic and both interpretations have problems:
If "Functions like [X]" is sufficient to make a spell count as 'X', then you would use the resistance line in the permanency spell. This interpretation causes problems because some spells were written without awareness of other special interactions with the spells they emulate, or without awareness of spells that emulate spells they give special interactions to. This lets people use unusual spell interactions to accomplish esoteric results, which may be undesirable.
If functioning as a given spell doesn't entail counting as that spell, then permanency can't affect these spells using resistance's line (though of course it may be able to otherwise do so). This interpretation causes problems because some spells were written with the understanding that they would count as the spells they say they emulate, and thus perform weirdly with this interpretation. While in theory the unexpected behavior could have similar results to the other interpretation, this interpretation in practice results in the badly affected spells failing to accomplish much of anything, including failing to do things they are clearly intended to do, rather than enabling much in the way of exploits.