Strange, I never noticed that change in the manual but it's right there in black and white. The only reason I can think of is that presumably the second Flarm antenna would be enabled and installed in order to cover a blind spot in the primary antenna so placing them close together would be kind of pointless.

So far the coverage of my Flarm installation seems good with just the one Flarm antenna judging by the range tool results. Good thing as on my ASW-15 the only place to put the primary was as far forward into the nose as possible since there's nowhere near enough room between the glare shield and canopy to fit it there. I was concerned that the rudder pedals might cause a blind spot but it seems to have decent range even straight back. If that weren't the case I would have to get a long cable because a secondary antenna would probably have to go back behind the trailing edge of the wing on the rear most bulkhead.