On the real hardware, there will be a way to reprogram the FPGA image if necessary to fix any bugs that are discovered after release. (This involves putting a jumper on the VERA board to enable access to the flash chip from the CPU.) So yes, if you would like to hack around you can, it is (will be) your hardware. Also the FPGA does have a feature where it can store up to 4 FPGA images in the flash chip, which could be nice for hardware hackers to allow the original image to be present in addition to their own creations.
Do note, that this will not be officially supported and normally users are expected to run original firmware. So if you mess up, it is on you.