How to enable "use low resolution" on Retina display for an Application when shipping it?

I'm not currently in a position to check, but it's likely that the presence or absence of the NSHighResolutionCapable key is cached in the Launch Services database. That's where most properties of an app which are specified in the Info.plist are stored. The fact that copying the app to a USB thumb drive worked seems to confirm that theory.

You might search the output of the following command for your app's bundle ID and then see if there's anything obviously related to high resolution capability:

/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -dump

If there is, then, after you modify an app's Info.plist, it might work to do:

/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -f /path/to/the/modified.app

If not, then perhaps the more powerful:

/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -kill -seed

If none of that helps, then (from our above comments) it seems that trying in a new user account works.

Takes a little more finesse, you need to reset the -user- domain.

/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -f /Applications -all local,user