But yes.. that's exactly what happens. If you have a Fastpass for Splash at 1:00 p.m. ... you're in a virtual line waiting your turn for 1:00 p.m. Meanwhile, you're also in the Standby line at Big Thunder Mountain.
So you can get off Big Thunder Mountain at 12:59... and walk right up to Splash, "cutting head" of the people already in the standby line for Splash -- But you're not really cutting ahead. You were already waiting in the Spash line, just virtually waiting. And they will indeed hold my spot in Spash, until 2:00 p.m.
Not sure what you're saying -- You say it doesn't cause the lines, and then you say it does cause the 30+ minute standby lines.
In fact, FP+ really makes all standby lines longer, because the majority of the distribution is going to FP.
Let's say you rope drop Magic Kingdom, and you're the 100th person on the standby line for Mine Train. With no FP system, you'd be getting on the ride in just 5 minutes. But because of FP, you may find that they are letting a couple hundred people cut ahead of you, and your waiting 15 minutes instead of 5.
Go back a few years, to the paper FP system, you can really demonstrate this effect. Back in the paper FP days, nobody had fastpasses for the first 40 minutes of the park. IIRC, the earliest fastpasses were timed for 40 minutes after park open. With FP+ system, with FPs being active right from the moment of park open, has caused longer standby lines right from minutes into park open.