Hi bigzer,
Thanks for bringing these to our attention, I've made sure we have visibility on these issues.
On the issue of 4K Output size, this is not used at this time for performance reasons. If 4K is very important for an asset such as skyboxes or macro detail, you can export the maps in Designer and import as regular textures in UE4.
As for the build size, the vast majority of that 12GB is going to be the Unreal Engine itself. The Substance Plugin is only a few megabytes of that total. You could reduce the footprint by selectively removing plugins (as an example if you don't use source control, no need for P4/Subversion plugins), but we want to stay as close to the UE4 release builds so it's easier to users, so we will provide a build that matches what Epic releases.