Currently the flags are settable only when using a debug version of platform, i.e. loading from the platform-dev component.
The easiest way to toggle these settings is via url query string:
?shadow: use the ShadowDOM polyfill even when native ShadowDOM is supported; note this also uses the CustomElements polyfill.
?register: use the Custom Elements polyfill even when native Custom Elements is supported.
You can check what's enabled this way:
if window.ShadowDOMPolyfill is defined, the ShadowDOM polyfill is in use.
if CustomElements.useNative is true, the native version of CustomElements is in use.
if HTMLImports.useNative is true, the native version of HTMLImports is in use.
I've asked @dfreedm to improve this a bit such that these flags can be used with the non-debug version of platform.js.