I think also a reason that these are smaller is partially due to a lack of early root development. Would suggest using a nutrient solution aimed at promoting root growth, and as others have said before, graduate the seedlings from smaller containers to larger once they've grown some. By filling the top of your containers with coco coir, the first couple of weeks of growth of the seedlings could be stunted as they can't immediately grow roots to the bottom of such a large container to access the rich soil there. Autoflowers are going to be less forgiving, because they're not going to fix themselves after going into flower.
Good luck with the rest of your grow 😊
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