There are two approaches.
Qt Creator Project Settings
For projects you've already created and don't intend to change, you can add "CONFIG+=c++11 warn_on" as a qmake argument in the project build configuration in Qt Creator:

You can then propagate those settings to shared project settings that become the default for all projects whose builds you haven't configured yet.
This is most helpful if you have lots of projects that you don't wish to modify.
Templates
You can create new projects from a template that has the settings you want. The template includes the prototypical files that constitute a project, e.g. the .pro file, source/header files, README, LICENSE, a default icon, etc. - anything you wish, really.
Qt Creator templates are built up of simple text files that are preprocessed by Qt Creator to substitute entries from the wizard. The wizards can be described in two ways: an older XML-based format, and a newer JSON-based format. See the documentation for more details.
I have an example of a simple XML-based wizard that I use to quickly create StackOverflow answers:
https://github.com/KubaO/stackoverflown/tree/master/qtcreator-templates
I'd like to have the compiler flags -Wall -pedantic -std=c++11 on by default.
Instead of using platform-specific options, use the cross-platform configuration options. The template should have the following in its .pro file:
CONFIG += c++11 warn_on
These are documented.