Voltage difference between two individual voltage sources
If the RPi is floating, then your measurements are meaningless.  That is because the voltmeter is providing the only connection between the two.

You haven't said where the 3.3 V of the RPi come from, but if from a isolated power supply, like a wall wart, then it is floating.  In that case you have to connect the two grounds for the signal of one to be meaningful and not hurt the other.