I agree that the home directory is the most logical place for files like these, but it would still be nice if they were in a consistent place. That way, if you wanted to delete your preferences for a specific application, you know exactly where to go without searching around. Personally, I think this should be enforced by the operating system instead of leaving it up to the developers.
It seems to me that my definition of an embedded device is different than the developer of this framework. Just because it is headless, doesn't necessarily mean it is embedded. A Linux server can be considered embedded, if that was the case.
The ESP32 is an awesome chip, but it is a beast. Dual-core, with Bluetooth, wifi, and everything else you could think of. I wouldn't call that your typical embedded device.
But, as things get cheaper and more power efficient, my definition will be antiquated and wrong, if it isn't already.