Can I change the default URI scheme in media.variables.inc?
Changing the code in a third-party module is never a good idea: All the times that module is updated, you should download the new version, edit it to change the code you altered, and update the copy used in your site. This means that, in Drupal 7, you could not use the Update manager module to automatically download, and update, the copy of that module.
If then the module code is changed not to use those constants, you should look at the new code, and see how changing it.

Those constants are probably used as defaults for Drupal variables. If those variables can be altered using the settings page of that module, then altering the constants is not necessary. 

There are other ways to alter the output of third-party code:


If the module is using those values for a form field shown in a form, another module can alter that form by implementing hook_form_alter(), and associate a different value to that form field.
If the module is using those values in a theme function, another module can override the function used for that theme function, implementing hook_theme_registry_alter(). In Drupal 7, it is also possible to implement hook_preprocess() to alter the variables passed to that theme function.
If the module is using those constants to set a variable used in a preprocess function, another module can implement hook_preprocess() to alter that variable.