I also have a Mini3D and use it exactly as you described, my projector (Sony VW85) doesn't have a lens memory so the Mini3D helps a lot in this matter. Just switch between the different aspect ratios with a single click on the remote.
I also use the NLS feature for 16:9 movies and i think it does a great job, personally i don't mind the small distortion of picture and rather fill my entire 2.35:1 screen without any black borders.
Havn't seen any noticeable pq loss using the Mini3D vs zooming with the projector.
Sony VPL-VW550 | DNP Supernova 08-85 116" 2.35:1 | Lumagen Radiance Pro 4440 | Pioneer SC-LX89 | Oppo UDP-203 | Zappiti One 4k HDR | PS4 | Audio Pro/Pioneer 5.1.4 Atmos | SVS SB-1000