I would see this as ruining all of the enjoyment since the games are meant to be played for story, and are often simplistic in terms of gameplay.
You could say this about every game (not limited to RPGs or story-based games) that someone was speedrunning at one point or another: why are they doing this? Well, if it is entertaining for them why not?
"Story-based" is not a title that dictates the game genre, mechanics or gameplay. So I don't know where "often simplistic in terms of gameplay" is coming from. You can have story-based platformer games, puzzle games, first-person exploration games, point&click games, JRPGs, action RPGs, and many more.
Okay, yes, RPGs are usually made for the story and sometimes they can have simple mechanics... but this is just a perfect opportunity for speedrunning. The added complexity of trying to fit the game into a short timeframe gives a new method to enjoy the game by, and expands upon the mechanics no matter how complex they already were.
And talking the very long RPGs, Bringing down the time of a 60 hour beast to even something like 10-20 hours is a feat of all it's own. Everything that is done is about shaving off seconds into minutes, then even hours saved. There are no simple routes, but grand plans in play with these.
(But this is coming from someone who quite likes the routing process.)