I agree with you Dan about the ideal being a properly mapped ECU and perhaps these folks will get to look at that later on. But we must remember that the S&S VFI module in the M3W is predominantly Closed-Loop, which means it can adjust the fuelling to keep track with the pre-programmed 'goal' by increasing injector durations - admittedly within relatively narrow parameters - to keep good mixture control. I' hope that the increases in fuelling required to maintain safe AFR's for this type of kit should be within the capabilities of the factory ECU self-adjustment scope.
But I am 100% certain that a 'mappable' S&S VFI unit is what we need next and of course those are readily available from S&S, complete with the required software. But I have heard from a couple of sources now that when fitted, these 'open' units don't allow the engine to even start, so clearly there is something technically clever built into the M3W setup to prevent a change from the 'locked' VFI module fitted by the factory. It can clearly be easily undone (witness the Mark Reeves factory 2.3 car, the Hesketh-24 and now the new Matchless V-Twin), but that bit is harder for the likes of us customers to work out for ourselves! Which is why we need some independent expertise from the likes of Garage56 to help us!
I too think the pipes will look better with black heatshields, but in terms of length I'd guess from the pictures that the silencer section is about 4" or 5" longer overall, mostly at the front rather than the back. Perhaps looks drove the factory design rather than performance - and to a certain extent I can understand that - but these new options seem like a fair compromise to me.
Scary info about those rear cylinder exhaust valve guides though - man they must get hot

I've found a picture of the black heatshields in place too...