I imagine that Custom Origins will miss out on any unique abilities and items relating to the Origins, Astarion getting Vampire powers, Lae'zel getting herself a silver sword, Shadowheart unlocking her memories and true identity, Gale eating magical artefacts, Wyll's Pact with Mizora (we see a consequence of failing to uphold it with his new look) and Karlach with her infernal engine. These give a unique spin to the class and race combination discouraging from creating doubles of the same class the reduce the chance of unique in game moments.
