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Not exactly. Performance improves when switching to a file system that has generally better performance. It just so happens that ext4 was chosen and it just so happens that's a "Linux file system" on a Linux-based device. I suspect that you would also see a (much smaller) performance boost with the exFAT file system if the Kobo shipped with the necessary file system drivers in the kernel. Which it can't cheaply do for exFAT, Microsoft has that locked down with patents. If the device had support for BSD's FFS I would expect even better performance.
The fact that a Linux PC is being used to manage the device is unimportant. You could install ext4 support on your Windows PC or your Mac and see exactly the same performance improvements. Although I think you would have to create the device file system on Linux anyway...
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