Dual Booting 10.11 and 10.9 - Spotlight Problems

I have El Capitan and Maveriks dual booted on my system. When I do Spotlight searches on El Capitan for apps it pulls up apps on Mavericks and vice versa. When I add Mavericks HD to the Privacy list of El Capitan's Spotlight preferences it ALSO makes that partition private on the Mavericks OS, meaning when I search I only get El Capitan results.

This leads me to believe that this setting to Privatize places for Spotlight is not stored on the individual partition, but might be stored...

Dual Booting 10.11 and 10.9 - Spotlight Problems