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While it is against best practice to load any spatial data as the SDE user (SDE should be
reserved for geodatabase administration), the issue here is in the fundamental design
of geodatabases. Feature datasets do not exist as database objects, and therefore
cannot have permissions granted in such a way as to quickly determine whether a
user has access to them. They are therefore, by design, listed at all times, and when
"exploded," permission to all the contained objects is tested (and if any are not
visible, then none of them are).