Disk size is given as number of blocks and block size. WinUAE does this correctly. The Amiga software fails in calculating the size in bytes because it uses 32bit integers (some programs even use signed integers).
The same happens when you connect a big harddrive to a real Amiga, too. If you don't want this problem, make smaller partitions or fill the big partitions with data until less than 2 GB space is left. Or use Amiga software which can deal with big disks. If you replace the old installer used by WW by the one which comes with OS 3.9, the installation will work correctly.
BTW, this happens with old Windows software, too. For example Need For Speed III refuses to save to a partition which has more than 2GB free space.