Dale:
I saw you posed this same question over at BMW-ST. I think the answer lies in this guy's response:
First,, is the offsetting U-joint angles.. If the front U-joint is operating at 2° & the rear U-joint is operating a ½° angle then proper phasing probably has little meaning.. The reason you phase U-joints is to have one operating shaft angle (therefore mid shaft accel/decl per rev) offset the shaft’s second U-joint angle (decel/accel per rev).. If the joints operate at different angles then phasing is much less effective..
Secondly,, sometimes U-joint phasing is purposely skewed due to shaft angle offset in another plane (ie the lateral output centerline is different than the lateral input centerline).. This is usually due to engine or final drive offset from vehicle centerline for one reason or another.. Sometimes a mis-matching couple of degrees of U-joint phasing can remove a vibration or harmonic set up from lateral misalignment or lateral angular mis-alignment..
There is also the phasing issue under drive torque.. You really want the U-joint phasing closest under shaft loading at nominal drive loads.. In a rubber isolator type shaft the phasing can be skewed slightly so the U-joints match up to closer phasing under normal drive loads..
That guy seems to know his stuff.
1) Angle of the U-joints: The purpose of the paralever set-up is to keep the final drive parallel (more or less) to the ground so the front and rear U-joints on our bikes are (again, more or less) at the same angle. Thus, phasing on our bikes seems like it could have an impact from that perspective.
2) Rubber insulated drive shafts: If you take a look at our drive shafts you'll notice that the front half of the drive shaft is, in fact, rubber insulated. When the rubber is torqued under load it would put the U-joints in phase if properly assembled.
My conclusion from this information is that it DOES matter. And, since all of the drive shafts seem to have the exact same offset, it appears as though the drive shafts were not manufatutred willy-nilly and that the BMW design and manufacturing engineers did take U-joint phasing into consideration.
That it didn't make it into the maintenance documentation does not, out of hand, mean that drive shaft phasing doesn't matter. The design engineers are not the ones who author maintenance manuals so the fact that it's not mentioned in the maintenance documentation doesn't prove anything conclusively. As things go from design to manufacturing to assembly to maintenance it would be easy for a small, yet potentially important, detail such as this to get lost in the shuffle.
So it does seem to matter:
1) Vibration. From what the guy says above, it appears as though being out of phase can introduce vibration. Obviously as riders we want as smooth a ride as possible. (H-D excluded.

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2) Wear and tear. If the U-joints are in phase then there's less vibration, a smoother transfer of power and less strain on both the U-joints and the rubber insulator. It could also reduce the strain on upstream and downstream power train components.
The final question is HOW MUCH does it matter? Got me.
I've had a few people contact me looking for drive shafts who were very specific about the dirve shaft having good rubber which indicates to me that's what failed on their bikes. Did those shafts fail due to improper phasing? No conclusive data but it does make one wonder.
In March I'm going to be pulling my RS apart to give it a spline lube. I got the bike with 25k and fairly complete service records so I have a high degree of confidence that things are as they were when the bike left the factory. I'll take a look at how the drive shaft was phased during assembly.
Whatever the case, when I reassemble the drive shaft, I'll be setting it up so that the half tooth gets compensated for in the phasing based on which way the rubber insulator is torqued under load. It certainly can't hurt.