Ok, I found now that MakeMKV includes a console tool.
MakeMKV> .\makemkvcon64.exe
Use: makemkvcon [switches] Command [Parameters]
Commands:
info <source>
prints info about disc
mkv <source> <title id> <destination folder>
saves a single title to mkv file
backup <source> <destination folder>
backs up disc to a hard drive
f <args>
run universal firmware tool
Source specification:
iso:<FileName> - open iso image <FileName>
file:<FolderName> - open files in folder <FolderName>
disc:<DiscId> - open disc with id <DiscId> (see list Command)
dev:<DeviceName> - open disc with OS device name <DeviceName>
Switches:
-r --robot - turn on "robot" mode, see http://www.makemkv.com/developers