Is it possible to set my own "new project" options without rebuilding
the CDT? E.g. I always want "-std=gnu11" and link with specific
libraries, need to add paths for headers etc.
You could create a new plugin and extend the org.eclipse.cdt.managedbuilder.core.buildDefinitions extension point. You will find some information how to do that in the help searching for the "Managed Build System Extensibility Document".