You may be interested in this topic if you care why MLT on timeline are twice as slow vs. intermediate renders.
I personally hate intermediate renders. “In my professional life” I render (ask editors to render) scenes as proxy and insist on final product to render from the source material. But that’s just me. There are different ways to go about production and disk space is cheap so looseless intermediate renders are OK.
Shotcut support for multiple timelines (MLT on MLT) is pretty basic.