A null magic mantle + Mr runes (25+8+8) are more than enough a counter for sorc shoes early if magic damage is really a problem (it isn't).
You absolutely don't need to finish mantle into a merc shoes.
It is pointless to get merc shoes over ninja tabi when u can get the same tenacity from runes (the only exception is when against full ap comps which is an auto loss for them anyway)
Get mantle and sit on it, your natural health gain + scaling Mr will complement it until you figure into what you want to finish it.
Magic pen needs to be strong because magic damage is mostly restricted by CDs and resources and it is not as reliable as physical damage (skill shots).
I don't know how this "magic pen is op" nonsense complains have started.
Dodging 1 skill shot and having 1 Mr item will make any ap champ unable to kill u while u auto him to death as he waits for his cds, getting lost health back in the process thanks to lifesteal.
Malph full rotation will not kill you if u had 1 Mr item. And he will not have enough mana to full combo u if he kept spamming Q to get u low enough for a combo kill.
I spammed lot of support malph recently with mama rune and spellthief so I know his mana spam issues even with said setup.
It will be harder for him to spam in solo lane for sure.