I've given up on that entirely.
Doesn't work the slightest bit.
However, what *does* work, and reliably too, is not using USB link to download the compiled sketch.
Rather, assuming that your Galileo is also on the (same) network as your Arduino IDE, you can rewrite the loader script to use SSH to download the sketch and start it.
This thread Partial solution for Arduino w/eglibc-based Galileo image which is in a slightly different context of making an eglibc Linux image work with the Arduino, contains the (Linux) version of the SSH download script.
Making this work for Windows is left as an exercise for the reader, but since it also uses an /sh shell, this should be trivial.
(And agree with your general point: the Linux image is pretty stable, albeit with some non-working parts in the standard Intel image. The Arduino integration could best be described as "unfinished")