The OP is 100% right that ninja's biggest architectural insight is the "assembler" metaphor. I came to this same conclusion in https://lwn.net/Articles/706404/

Sad to hear the overall experience has been so negative for him. Ninja has certainly had a large impact! I can relate to the open-source burnout, even though I've experienced only a tiny tiny fraction of it compared to the success of Ninja.

Re. speed, I wonder how much of Ninja's speed over make is thanks to Ninja's "deps log" binary format. In my (fabricated) benchmarks, Make spent 98% of its time processing the compiler-generated ".d" files that are used to track dependencies on header files: https://david.rothlis.net/ninja-benchmark/