The rewriting of the YAML section isn’t a new thing. It has been happening since we introduced the API (used by plugins) to read and write YAML.
You are just noticing it now because you indirectly interact with that API (and the underling parsing library) every time you use the properties UI.
“Rewrites” can happen any time that API is involved (of which I can’t foresee all future and third party use cases) and again we are fine as long as what is written is semantically the same to what you manually input.