Hi,
In fact, KinetisFlashTool call blhost.exe to send command. The blhost application is a command-line utility used by the host computer to initiate communication and inject commands to the Kinetis bootloader. The application only sends one command per invocation. So you can use batch file to do it.
The blhost's user's guide is in bootloader2.0.0 package, or you can find it in NXP website.
Regards,
Jing