According to the 'L' and 'R' designation at the end of the serial numbers on the back of each pair of NS-1000s, the tweeter/mid pairs should be on the outside
I don't think this is intended to actually place the L speaker on the left, but the L indicates the placement of the mid and tweeter on the speaker itself.
In the studio, you will see that the mid and tweeter are often always placed on the inside. (also on the manual they show at the inside)
I suspect that Yamaha saw this as a problem with many, and therefore released the NS1000X with everything in the middle.
- These are just thoughts of mine, I could be wrong, what matters is how they sound best to you.