My setup is exactly like this guys:
Inductive cellphone charging without voiding warranty - Hack a Day
Not sure if there's a post limit before people can see links (like on PreCentral). If not google: Inductive cellphone charging without voiding warranty
After trying your tests (trying the phone touchscreen in different places while the coil is on the touchstone) and reading your attempts to lock it to a voltage problem I tried some things.
I put the magnets back in my setup and measured the voltage coming from the power leads (the exposed contacts). I measured a steady 5.6V. I then took the magnets out and measured. The reading obviously differed based on how centered the coil was on the touchstone but the readings were generally between 4.5V and 5.6V. I moved the coil to a point that was ~4.7V then plugged the phone in. It worked perfectly. This points to an over voltage to the phone as the culprit. I'll calculate a circuit tomorrow (probably) to try maintaining a lower voltage to the phone.
To answer your other questions:
If placed as high as possible in the back, the bulge isn't noticeable and the 2 wires coming out of the bottom are the only clue something has changed. If placed near the bottom, the lower latches are nearly impossible to latch and that makes it very noticeable and the back seems prone to pop off.
The phone holds on pretty weakly compared to my Pre. It does snap into place when the magnets are present. (I noticed in your writeup you call them metal stubs. Mine are magnets and the polarity is marked with a + sign which should face out from the phone).
Mistakes/gotchyas I've made/seen so far:
When reading pinouts online they are showing you the jack (female/phone) part. Mirror the pinouts to solder the plug (male) side.
Put magnetic stubs in backwards. Causes the phone to go cockeyed on the touchstone. The + sign etched in the magnet point away from the phone when everything is put together.
The D+ and D- pins need to be shorted on the USB plug (male) part. Just solder a wire between the pins (don't mistake it for the unused Pin 4). (Plug, not the jack which is the female part on the phone).