I personally just do boring USB transfer of files instead. Users have reported issues with Calibre modifying KCC files and breaking the formatting, fixed layout books like comics/manga are different than normal reflowable ebooks.
I only use Calibre for normal ebooks.
Maybe in the future, KCC has command line versions as well. It's all Python.
I think calibre plugins are all python, in theory that should work. In practice, who knows.
How do you do USB transfers without Calibre?
You just drag and drop the mobi file into the documents folder on the Kindle.
If you are on macOS, you need the Amazon USB File Manager app to do that on newer MTP based Kindles. Older kindles just used ordinary USB mass storage protocol. Link in readme.