Let's analyse two options as to why the chasing team bats first in super over.
The team that won the toss chose to bat first, but failed to win the match even with the advantage of toss. So exactly the opposite decision is imposed on the team in super over, as such the team has to chase the target in super over.
The team that won the toss chose to field first. So their decision is to chase down the target and failed even with the advantage of toss. So exactly the opposite decision is imposed on the team.
I believe this is because the team that scored without the advantage of the toss have a superior position in the draw than the one who got into the position with the toss. The batting order is reversed on the belief that the superior team is given a priority in conjunction with oppononent's previous decision.