Sorry for the very late reply, I somehow missed your post.
1. I see numerous feet in the first section; is this a "pick the kind that suits" you kind of deal, or do I need all of them? I'm a bit lost here. I see the holes for the standoffs. (is there a sample image someone can show?)
Sorry for making it so confusing, I should have made it clearer, basically... The large piece is required regardless of which PCB you are using. The feet spacer is only required for Phantom to accommodate the Teensy. Now, the two long pieces are required if you want to have a flat board, these can be used to balance out the positive incline by bolting these to the side close to the user. The circular ones are used to give a larger positive incline, just assemble them in a conical shape, number of layers used depends on the incline you want. I hope this clears up doubts, I'll post an illustration to clarify.
2. How is the notch for the USB plug supposed to work? The teensy has the plug on its own board. Are you accommodating people who want to add a short male to female cable here?
Yes, if you see, the notch is narrow on the edge of the case outline and then expands to accommodate a SparkFun miniUSB breakout board which you can bolt down into the large feet layer (There are four small mounting holes).
3. Just to confirm, if I'm using the plate from mechanical keyboards fro the phantom, then I skip swill's tool, use the plate spacer and the spacer needs to match the plates thickness?
If you use the plate from MK.com then yes, you don't need to generate a plate layer, you will however need at east one bezel layer
4. The instructions say to use a bezel, layer F. Layer F in the SVG is "QFR Controller Spacer" - G is the set of bezels. Is this an error?
Yes, typo, should be Layer G for Bezels.