When using Processing System 7 v4.02a the "Enable GPIO on EMIO Interface" cannot be changed in the PS to PL Interface configuration dialog box.
This option can be found under "General" in the "User" tab.
For versions 4.01a and below this works as expected.
As a workaround this parameter can be set in the MHS file:
PARAMETER C_EN_EMIO_GPIO = 1