Since the actual yaml file is small, why not add an option to transfer to the device as well. Then maybe the option to download from the device website or a recover option (by pointing at a ESP device IP) in ESP Home itself.
yes yes this is one of the most annoying things about ESPHome. If i lose the config and want to change it on one of my devices, i have to manually rewrite the whole config file.
Sounds good if it is in fact this simple.
=> github private repositories. 
Basically, for all configs.
Berkeley UNIX kernels were built like this decades ago. The configuration file was just compiled into the image with some distinctive markers, and you could run the strings command on the binary and recover it. Well worth it. And ESPHome could expose an API to return this string.
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What about making minor config changes? Only using the compiled modules? While testing stuff I need to install esphome again for every minor change.