Our shower is 48"x48", the drain can be positioned either on the left or left-top corner, but not in the center because bathroom main drain goes through there. Can I still use Schluter is such setup, from what I've seen on their product page, 48"x48" floor substrate comes with only center drain?
You can get a Kerdi pan with offset drain, or trim an oversized pan so that the drain ends up where you can connect it. Or you can get a pan with a line drain, along one edge of the pan.
Since the trays are sloped, trimming it asymmetrically might leave you with a height difference between two sides. You can use mortar to fill the (small) gap.
Alternatively you can use a linear (line) drain