You can use both variants as needed. In my BeginnerExample (step 2) the flower is not indexed. Here also only some points of the triangles are identical. In paperplane I used indices.
My addon Addon. Produces almost infinite many time-varying geometries with functions I had created first with the old geometry, and after a hint both as indexed and non-indexed geometry . Only with the non-indexed geometry the explode mode is possible.
So it depends on what you want to do and which variant is more suitable.
another example Magic Box