It's interesting how changes in book delivery can change book structures. With a dead-tree book, having the footnotes at the foot of the page is really nice. I used to complain about books with endnotes where they were at the back of the book. With an ebook, having endnotes is less distracting than footnotes (as retiredbiker said). But, especially for fiction (few footnotes), I like your solution. And, if I'm going to be messing with the book's code anyway, I might as well put the footnotes where I want them.
EDIT: Also, I like the structure of your actual footnote links. In mine, the <a... parts are structurally different from each other at source/destination. By keeping the id= part in the <a part at both places (as you do), it makes it easier to change the id= and href= points (by moving the appended "a" in each around).