Steve,
Sorry, I've been busy the last couple of days, but have been following this thread. Having just read back over the thread and also re-read the (currently very basic) Flarm Eagle quick-start manual, it does appear, as you say, that LXNavigation now intend to produce an upgrade option to 'PF + 1090'. Pretty sure that option wasn't in Version 1 of the guide. This would be relatively easy by adding the standard 'PFC' 1090 Module already used in Flarm's own PFC.
I haven't personally seen the physical size of the Eagle yet, but judging from the size of the connectors, this would almost certainly need to be an either/or alternative to adding the second Flarm Receiver. I would suspect the additional cost would be in the same ballpark as the existing price difference between the current PF Pure and PF Core - i.e. in the region of £500. It might of course be cheaper, but still much more expensive than PilotAware, and you will still need a 1090 antenna.
With regard to the LEDs on the FTDI lead, Ian is correct, the Green LED flashes to indicate received data, but I can't say without re-testing whether this flashes on receipt of GPS data or only on receipt of traffic data because I currently use a different lead in the plane with no LEDs (having donated my FTDI to connect our CFI's PFC to his PilotAware). I do have a spare FTDI lead here, however, so will try to set it up and test it tomorrow.
Best Regards
Peter