GPIO voltage depends where you are looking. The Tegra X1 itself is mounted on a module which may add or modify the answer to the question, and this in turn is mounted on a carrier board. Are you interested in the GPIO voltages on the carrier board? If so, many of them have a selectable jumper for 1.8V or 3.3V operation (much of the Tegra X1 is open drain and voltage depends on pull-up, and on the developer carrier board there is a jumper for some of the GPIO to select your choice of 1.8V or 3.3V).
The software which JTX1 arrives with is a mostly stock Linux SMP operating system. So to use the JTX1 without Linux would probably be a big undertaking. To use core affinity within Linux, I’m not sure what would have to be done…this is possibly feasible with minimal effort, but I cannot confirm (the question here is more about Linux limitations/flexibility than about JTX1 limitations/flexibility). In terms of RT, Linux has some pseudo-RT features, but these are not true RT (audio for example takes advantage of this). If you desire to assign one CPU core to some outside function, the architecture makes assignment of hardware IRQ difficult on any CPU except core 0, and so something like an FPGA might be a better choice there (this could for example connect via PCIe). If your outside function for a given core is software-only, without need for hardware IRQ, I believe this would be much easier to deal with without adding an FPGA or other outside micro-controller.