Moving the Arduino headers further from the RPi header: it won't work since the user won't be able to plug the HDMI cable.
Placing the RPi header "at the back" of the board, rotated 90 degrees: it could be a better fit, but still the Arduino headers will touch some components in the Raspberry Pi
Do not populate the headers by default: problem is that main target will be the Arduino users so most people will have to solder them themselves.
Using longer headers: could work, soldering the tips of the header pins at a certain high (we need minimum 5mm more than now). The header should be soldered so it sits flat when mounted over an arduino. See pic.
J10 & J11 touch the HDMI connector when the connector J14 is connected to Raspberry