They are spontaneous...if you experience spontaneous jhana/kundalini. Everything else, is like reading someone else's story. Kind of like which came first: the chicken or the egg. I am sure that many systems include them, either with intent to manipulate energy, or more like vestigial cultural remnants (like you see in karate katas).
Apologies if I step on any toes. I don't know anything about 'institutionalized' mudras, and am speaking from an 'experiential' viewpoint.