The Flex is designed to be powered completely by a single USB2.0 +5V 500mA line, hence the 32 LED limit.
The Neopixel 8x8 matrix is 64 LEDs. The Flex would have to be flashed with the standard Pro firmware to remove the limit (which I believe the manufacturer will do if you specify that in the order).
The danger then is letting the matrix pull too much power from a single USB2.0 +5V line. You would have to power the matrix independently, or bundle a second USB2.0 +5V line to the Flex.
USB3.0 and USB3.1 +5V lines are 900mA so the extra line would probably not be necessary. It would be nice if the Flex firmware could detect the USB version and set the limits accordingly.