We apply our theory of partial flag spaces developed with W. Goldring to study a group-theoretical generalization of the canonical filtration of a truncated Barsotti–Tate group of level 1. As an application, we determine explicitly the normalization of the Zariski closures of Ekedahl–Oort strata of Shimura varieties of Hodge-type as certain closed coarse strata in the associated partial flag spaces.