That's what I thought you meant, just wanted to play it back to you to make sure I understood.
It's a simple mod. You're right, the input will always be loading the guitar signal, but since the input impedance is 1M shunted by 100pF, the loading effect is less than 10ft of cable going into an amp.
The mod can be implemented the same way whether you have a breakout board on the stomp switch or not. The switch terminals are numbered like this (same orientation as shown in the build docs):
1) Disconnect the wire that goes from the Input on the board to the stomp switch at the stomp switch end (either from the breakout board or the switch).
2) Connect that end of the wire to pin 3.
3) Disconnect the wire that goes from the Input jack to the stomp switch at the stomp switch end (either from the breakout board or the switch).
4) Connect that end of the wire to pin 9.
If you're implementing this mod on a new build, you can use a DPDT stomp switch because the left column is not needed.
If you're really concerned about loading, the best place for a buffer is at the guitar.