I'm talking about the physical book, not the words contained within.
> When I buy a house, I can make modifications to it.
When I buy software, I should be able to make modifications to it.
> Microsoft probably wouldn't care if I somehow reverse engineered Windows and modified it for myself only.
That's explicitly prohibited by the license. Whether or not you think they'll enforce the license in your case has no bearing over the fact that it does violate it, and free software advocates argue that such licenses cannot be nonenforceable.
In any case, patents are a separate issue altogether. So is copyright, actually - free software licenses are a way of twisting current copyright law into doing the opposite of what it was meant to do: provide freedom.