My configuration is a Pioneer AV Amp for all but my record deck which connects directly to my Elisit-R, this is also connected to the front/left preouts of the Pioneer and drives my B&W CM8s directly for watching movies on my PJ. The rest of my speakers are also B&W, but from the cheaper range. I have no problem when using 5:1 and the CM8s as the front speakers, but I also get the benefit of being able to listen to my recird deck via a very much superior amp for stereo.
The setting of the volume control on the Elicit-R is important and should be set to the same position used when callibrating but can also be "tweaked" when watching a movie to fine tune against the centre speaker depending on vocals and special effects and personal preference for individual films.
I certainly don't have an issue with anything the Pioneer might be removing when watching a film, technically it may be removing something, but if it is I can't tell.