If I want a new filesystem, I can write it as a FUSE file system, or a kernel module, in such a way I can endlessly customize Linux to what ever I want. Why do the two other desktop OSs (Mac and Windows) not offer that level of customization? And even if they could I wouldn't be able to distribute my customized version.

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You can. OSXFuse is a FUSE based driver for Mac. On the Windows side there are open source FUSE solutions such as Dokan also.