The original public tools for mp4 did not make it easy to use aac audio rips. Mkv also has the perception of being able to handle a broader range of BR audio rip stuff - DTSHD and TrueHD being two examples. I don't know if those are widely included, but I know there was chatter about that.
I think the reality is that when HD ripping was first starting out the open source mkv container had greater support for certain things, so people flocked to it, and then the mp4 specs came up to speed but by then mkv was the de facto standard for scene rips.
I think there is also probably the "cool" factor that still occurs in these scenes where the more obscure and "tech savvy" format is the one that people like to use initially. I think nowadays pretty much every video player can handle any of the scene release formats so its not really an issue.
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