Instead of dealing with somewhat cumbersome command-line options it could be more user friendly to allow a text file with a JSON object to configure the compiler!
JSON can be regarded as kind of de facto standard for configs & co so Kotlin could take the bill.
A large project without build tool is hard to develop and unmaintainable in general. You can do it for your own pleasure, but do not expect your command-line code to be used or supported by anyone.
One can write the code to take a json file and invoke the compiler with the options specified in the json file.
That is easy enough that the compiler shouldn’t need to support that independently.