If you remove glkote.js but leave in glkapi.js, you should have a setup that works exactly like RemGlk.
I say “should” because it hasn’t been thoroughly tested in that configuration. But I think I tested it a little, at some point.
Yes, the organization of the code is kind of ugly. The startup sequence starts at load_run() in gi_load.js and zig-zags through the other modules. But they are in fact meant to be modular; they can be used as Node modules in a Node environment. Each one refers to the others through well-defined APIs.