It is worth taking a look at.

You really have to look at the different filesystems that are in use under Linux. If you are installing a recent distro, which, by default, would use the ext3 or ext4 filesystem, your transfer rates would be just a bit slower than using ext2. Why? Because ext3 and ext4 are journaling file systems, whereas ext2 isn't. I haven't heard of any complaints from users about transfer rates, unless they are using some personally modified file structure, or, they have incorrectly modified config files that deal with the setup of their file systems.
Anyway, the advantages of Linux file systems would far outweigh the milliseconds of lost transfer rates, if in fact your comparing Linux files systems with equal features as those of Microsoft.
As far as cool and quiet, I'm assuming this is one of the motherboard features that some manufacturers such as Asus have. I use Asus motherboards and have never used these features. You can control power settings from within the Linux OS, so I don't really have a use for them.