I haven't seen tests with encoders and Galileo boards. In order to choose an encoder that will work, you have to consider the current and voltage specifications of the pins in the board and the power specifications of the encoder.
If you take a look at the Schematic of the Galileo Gen2 you will see that the Digital inputs are connected to the 74LVC1G157 multiplexer and checking the datasheet of this component you will see the specifications that your need for make the encoder work.
i have used basic encoder ALPS STEC12E07 Encoder and it works fine with the galileo board.
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