% max health true damage is certainly an incredibly stupid idea, but it's supposed to be placed incredibly carefully on champions.
The best way to counter it would be to counter build the champion using it, or build items to sustain through it. % max health true damage on a squishy with a lot of life steal will be less useful than against a full tank nautilus.
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CounterPLAY. You can't counter build it. But each of the champions given % true damage have actually been given fair ways to counter play them.
Fiora - Reliant on hitting targets that are visible to the opponent. Positioning is key here. You know where she wants to go. If it looks open to her, either bait her out or keep out of distance until it moves. If it looks hard for her (dead behind you, for example), use that time to go aggressive. She's not going to be able to get to your back easily.
Garen - Only has it on one target at a time, target is known to everyone, and Garen can't even apply it to his lane opponent anymore. Well, not unless they've killed other than Garen. Plus, he took a major hit to a lot of his stats in exchange.
Vayne - The most controversial. The trickiest to figure out. And as awkward as it sounds, the best thing to do is never 1v1 her. That is her realm, her power, her arena where she rules. If you're an assassin, burst her down. Otherwise, find a buddy. Most people don't know this, but if Vayne is forced to switch targets, all stacks of Silver Bolts are lost on the previous target. So force her to keep switching. Make her find a higher priority, and kill her while she does so. She can ONLY 1v1 people. She doesn't have the luxury of poking or hitting with AOE abilities. Either wear her down from a distance, or take her down in a swift blow.