Is it possible to configure EMIO pins of zynq 7000 to 1.8 volts?
There are no EMIO pins, per se. EMIO is the internal channel between the PS and PL, which may or may not be pinned out to a physical pin. If you are talking about an EMIO channel that is pinned out to a physical PL pin, then the voltage definition of that pin is governed by the type of PL pin that it is.
On Zynq-7000, there are two types of PL I/Os -- HR and HP. You can see the voltage I/O characteristics in DS191. Both can support 1.8V.
Are you asking specifically about whether the Mini-ITX can set a PL Pin to 1.8V? Looks like Bank 35 is set to 1.8V. Banks 10, 11, 12, and 13 can be set to 1.8V if you short 3-5 on JP7.
Bryan