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It seems that currently the index set for reducible types can only be consecutive integers starting from 1.
sage: ct = CartanType("B3").subtype([1, 3])
sage: ct.index_set??
This is displayed also in the following example
sage: CartanType("A5").index_set()
(1, 2, 3, 4, 5)
sage: CartanType("A5").subtype([3,4]).index_set()
(3, 4)
sage: CartanType("A5").subtype([1,4]).index_set()
(1, 2)
So there is certainly room for improvement here.
