The error above and below happens because of static Flavor = Flavor and static Executable = Executable.
Is there a way to redesign this?

The only workaround I was able to find that works, is by restricting these Entities to classes rather than mixins. This means they cannot be mixed into another class while maintaining type safety, but can be much more easily attached to other classes similar to how Executable class is attached to Application class as a static attribute. It results in much more reasonable *.d.ts file sizes, and doesn't require maintaining class and interface separately. They should be overridable in web-app as long as each type is castable to the inferred type in the base Executable:
example: flavors getter expects to return an array. This means the base Executable definition should ensure that the type of each method is generic enough for our needs to support overriding.

export class WebappExecutable extends Executable {
    get flavors() {
        return [];
    }
}
export class WebappExecutableApplication extends Application {
    static Executable = WebappExecutable;
}

TLDR;

• Use classes instead of mixins for Application, Executable, Flavor, Template, will need to reconsider ContextProviders since they will prefer mixin functionality.
• Maintain base class interface as part of base class definition, overriding inferred types where necessary to be generic enough.

The application.d.ts file still seems very large. I will probably create a task for myself to investigate possible solutions for future work. Otherwise code looks good

Did you check that without this.constructor re-defining Executable in webapp startup will still work correctly??

Seems to work as expected