Hello Josh,
Take a blank project with your custom pin config from 1.1.3 and migrate it to 1.2.0-b1. Then you can use update pincfg file in 1.2.0-b1 projects. If your e2studio installation has only SSP 1.2.0-b1 installed, the pin configurator will be blank until you close and re-open the configuration.xml file.
Regards