The fit of the cover is admittedly a bit awkward. It is in fact narrower than the case, because the cover plastic sits to the outside surface of the rear flanges and then contacts the case just to the outside of the rails. This puts the flanges down on top of the rails. If you want to notch the bottoms of them so they mate to the rails, that's fine, but you can also just use the gap to put a little piece of foam insulation in there. Just center the rear flange plate on the machine and all should be more or less ok.
The next big revision to the plans will solve these quirky little issues with a completely redesigned base and cover. It will also give some more room for electronics. Look for a preview of the prototype in a few months. In the meanwhile, the current design works well, but it does have the occasional weird little thing going on, as you've discovered.