I think Riot has a balancing protocol against certain "free" abilities like Malphite's passive. That would explain why things like Teemo's E and Twitch's passive won't proc Spellthief's, Rylai's, or Liandry's, because passive abilities have the potential to be such a source of synergy that it could become a constant obstacle to be overcome.
Things like Brand's DoTs, a support's shields, or even an item's active would require a cooldown being used + either a spell cost or a gold investment. That being said, Mordekaiser can only charge his shield through abilities so he does burn the same resources as other champs to stack his passive, the only difference being that he uses health where most (all?) other shields would use mana. I could see them keeping Malphite's interaction being the way it is based on this track record, but Morde is in a different boat.
I see two possible reasons Riot would want this interaction on Mordekaiser. If Riot really wanted masteries to be something people think about this season, making that mastery synergize with his kit like that would pretty much make that mastery mandatory for Mordekaiser since it would work so incredibly well. The other reason could be the possible balance issues it could cause since this mastery roughly translates to Morde taking 8% less damage throughout a match.
I'm not going to actively defend either of the possibilities, but Riot's balance will always end up being absolute. Riot expects champs like Mundo to buy Spirit Visage, but were it not in the game there's no doubt that his ultimate's heal would be stronger. If Riot did believe either of the ideas mentioned, changing the interaction between the mastery and his passive would without a doubt result in Riot nerfing his shield.
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