I argued this should be the start of Morrison v2 either here or in a Batman thread, but it's not without its problems (I think JBatmanFan05 was the one effectively arguing the other side). The second missing chapter reveals the nature of Darkseid's trap well before it's revealed in RoBW (both the horror of the monster and the bush machine Batman in #2, for example, are intended to be confusing but would be pretty clear when read after The Missing Chapters). Likewise, Tim's part of the story is being the Bat-representative at the end of the Missing Chapters, and he doesn't appear again until RoBW #5 - if you put them first, that's a long time off between appearances and may lessen the impact of his role. Also, using The Missing Chapters to replace Final Crisis in the chronology omits some of the Metron stuff from FC that helps explicate the end of RoBW.
I would be fine with The Missing Chapters kicking off the second volume of Morrison omnibuses, but I've read the stories before (multiple times!) and support collecting them in Bruce's chronological order (I get the argument for publication order, but I like narrative momentum and would prefer having each arc collected together). However, I think a 2-3 page FC recap, then putting all of the RoBW and Time and the Batman material in the latter half of the collection would be a perfectly fair and reasonable choice.