Hello,
I don't think BS3 MKI will pass through the 3D signal correctly. So bypassing BS3 for 3D sources couöd be an option, but you will discover resrictions. You will not get BS3 onscreen displays anymore on the screen (menu displays, volume level etc...). You could use a HDMI splitter to split the outgoing signal coming from the player into one giong to BS3 and one going to the beamer. Maybe there will be a problem switching the beamer input between the two hdmi inputs (one from bs3 2D input, second direct 3D input) using PUC.
I use this solution, but I'm using Beo6 to control the beamer, as my beamer isn't in the PUC list.
hfat