It's a bit of an unfortunate coincidence. Mark of the Mountain Drake increasing true damage was a bug that they fixed, whereas the Backdoor Plating change just happened to be on the same list. I really heavily dislike Backdoor Plating reducing true damage, particularly since there could've been an interesting extra feature for true damage as an enabler to backdoor strats, but right now it's a necessary evil (Riot wants to prevent backdooring from being too effective, especially for junglers and marksmen), poorly implemented (Rito needs to contradict themselves on how they want true damage to work).
Personally, I think the best solution at this point should be to just change Mountain Drake to a standard damage amplifier, and subsequently buff it (e.g. to something like 30 / 40 / 50%). The buff would still be able to work with some consistency on epic jungle monsters, while also playing nice with Backdoor Plating and Baron Nashor's damage reduction, which it currently ignores (and that might lead to another special-case change if Baron capping gets accelerated too quickly).