Might I suggest investing in a Dremel or some other stupidly-cheap rotary tool? Or just go old school and cut with an Xacto blade.
You're ordering stuff from a Maker site. I assume you must at least have some Maker ability if you are dealing with a Pi. So...MAKE. The low-profile reader doesn't work in the PiBox either, but I fired up my $8 Harbor-Freight rotary tool with a sanding drum and polished that sucker right down (About half way through the thickness of the bottom plate) to where it would fit. And not only does it fit, it looks mostly stock.
Good luck. That adapter is far from a waste, and far worth the effort to make it work.
When you open your mind to the impossible, sometimes you find the truth.