xkcd was kind of answer to your "if there should be a simple flat file format that keeps all the information COLLADA and gltf scatter all over god's green earth into simple data records" text.
Sure, there is nothing wrong wanting something simpler that works for you and implementing it. But pretty much there always will be some extra feature/thing that does not work for somebody else. And then it won't be simpler for them to use this new format.
I'm not aware of any serious game engine that uses gltf as runtime format. I don't know exact history but afaik it is just a claim from khronos (about usability as runtime format). Who for some reason decided to push into web space and decided to create json-like text/binary format for loading into webgl. I guess xml-based collada was not good for them. So now we have json based format. What's next? Yaml? Protobuf?
I am aware of md5 format. I have written mdl/md2/md3/md5 loaders for fun. Those are real runtime formats for idTech engine. But again, what works for them won't work for everybody. Thus the xkcd comic strip.
Have you seen OpenGEX
from Eric Lengyel? Not a binary/runtime format, but should be very usable as intermediate import format from 3d software. Here's an comparison with collada and gltf: https://opengex.org/comparison.html