Thanks Josh for explaining. 
The latest version of the CLI is beta 11 and it is using JS as the default for all starters. Each starter and the conference app have typescript branches if you would like to use typescript. There are some config changes that need to happen so make sure you either copy from that branch or compare your existing code.
The way the starters work is you insert the www/ folder from the starter you want to use into the "ionic2-app-base" folder.
https://github.com/driftyco/ionic2-app-base/tree/typescript?files=1
https://github.com/driftyco/ionic2-starter-blank/tree/typescript?files=1