The 696 midpipe will work on the 1100.... I sold mine to ungeheuer so he knows first hand.
Confirmed, its a direct swap. Although I since went another route and sold
DoWorkSon's 696 midpipe to yet another M1100 owner.
While it would be nice to get rid of the midpipe it is not necessary to do so because of the EE installation. The default setting is open and I would doubt that leaving the midpipe in place has any negative effect.
Not necessary, but nice nonetheless. The negatives of the flapper IMO are these: Its an eyesore. It acts as a heat-sink. Even open it still must be disrupting the gas flow to some degree.