I could be wrong, but this one, in particular, I envisioned to be a measure to at least make looting a hacked account a bit more difficult, (though the original devs also didn't seem to think creating tons of alts would be a thing, either, admittedly).
When you say "seemless", what do you mean? There are co-op zones, where players of all alignments can team freely. The hero or villain-sides are, by design, exclusive to those leaning toward one side of the hero<->villain scale.
There are quartermasters in some zones that do sell every type of SO, AFAIK, unless you mean something else when you say "all option enhancements". From a thematic standpoint, the origin-specific stores hero-side at least make some sense...