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This is surely a touchy one as I've met many Linux systems administrators and while there is a lot of consistency, there is still a bit of "special sauce" that gets smothered on top; especially when we touch about base OS partition. Generally, I tried to stay out of these religious arguments. Besides, many teams have already made decisions on how they lay down the OS. Of the four main areas that Hadoop distributions need disk space for (i.e. bits, config, logs and data), I usually subscribe to the model of letting the bits, config and logs, as identified above, be persisted in their default locations. As there are many Hadoop components, it is easy to imagine a big requirements on disk storage. If the Linux administrators have a strategy for this, then great, but it does need to be thought about.
One strategy I've seen well is to have a separate mount point (and underlying disk) devoted to /var/log for all components, not just Hadoop ones, to log to.