How to work with analog readings using RPi and Firmata?
It does not appear that Firmata has proceeded with the ability to change the analog reference source. You referenced one of the issues opened for it, but I don't see anywhere where it committed to the current master branch.

There's no way for an Arduino to read a voltage without some reference, and as you are experiencing, the default reference is Vcc. That means everything must be compared to Vcc, and if you compare Vcc to itself, you will always find out that Vcc is equal to Vcc. 

The pull request to implement is here, so you could play around with it yourself.