running multiple *.kibot.yaml files is possible by executing
a bundle eg kicad-exports -c config/bundle/documentation.default.kibot.lst. The file ending .kibot.lst is a used for textfiles listing all kibot.yaml files.
or with wildcards kicad-exports -c config/*.kibot.yaml
I am currently already working on v2.2. As kibot 0.8.0 is currently in the pipeline this is something I am waiting for and it will enable some nice things. Additionally I am working on more predefined config files which will generate outputs fitting special needs, eg a BoM in a format compatible to JLCPCB or plotting PCB renders in oshparks famous purple/afterdark colors. so stay tuned!