I actually provided this as feedback to pi-top support by email on Aug 11. Normally got prompt replies from them (thank guys) but no reply, so reminded them asked for acknowledgement on Aug 16, still no reply by Aug 31 so sent another email reminder. Still no reply so we're getting some insight into the state of pi-tops email support at present alas, and I'll post it publicly here:
My out-of-box experience:
Very well written and interesting report.
I thought I might give you some of the answers to questions you have raised:
The hub controller acts as both a power supply for the rpi and an interface between the hdmi output of the rpi and the screen.
The connections labeled spi mosi, spi miso, spi clk and spi cs1 make a connection of the so called spi bus of the rpi with the hub controller. This allows the software of the rpi to talk to the hub controller. On the pi-topCEED this connection is really only necessary to adjust the screen brightness. As long as you are happy with the brightness of the screen, the pi-topCEED works perfectly well without this connection. If you are using pi-topOS and have made this connection, you can control the screen brightness with the brightness keys.
Once you have been getting used to the pi-top and linux you might want to also use plain Raspbian Jessie on your rpi. If that is the case, there is an explanation of how you can control the hardware of the pi-top with this standard OS on github.com/rricharz/pi-top-install
I agree with the original author. The out-of-the-box experience is mind-numbingly silly. All it would take is a little more text to tell you WHY to attach the GPIO, and I agree that the HDMI cable is very stiff. I got it to work right away, but damaged the screen when I pulled off the screen protector. It buckled and put a dimple in the screen. For about $115 (US) I suppose I can't expect better, but it was mildly disappointing.
Am working now to create the application I intended, but found this note and was very supported of his experience.
One more question: My pi-topCEED has a full 40-pin connector. Makes it completely useless if I choose to use a RP v1. That was frustrating. If you make a version with separate connectors (for power, the special screen control, etc) it would be nice to market it as an option.