have you tried flipping with code? in gamemaker.io , sprite will be flipped based on origin point.
i believe there will be a way to flip sprite based on origin point. otherwise defining origin is not really useful.
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In Godot, the origin point is mainly used for Y-Sorting, flipping only flips using the texture's width / height . But yes, you can use code to flip the texture and then move it a few pixels in the X axis, but it would've been better if the sprite was already centered. Anyways, I fixed it really easily so no worries about it :)