Another issue that comes up in alliances (SkyTeam springs to mind) is that you'll have a lot of B6 fliers trying to redeem points for the F trip on the other carrier, while the partner can't redeem for F on B6. This came up in SkyTeam when all the US-based carrier FF members started redeeming like crazy for the F seats on KE and AF. Even the higher redemption prices didn't deter the passengers, and AF/KE basically ran out of seats with nothing to show for it for their loyal passengers.
LY has partnerships with several carriers, including DL and AA, so they aren't so alone right now as to need B6.
As to the longer flight in F thought, for Icelandair and Aer Lingus the JFK-West Coast flight would be almost as long as the KEF/DUB/SNN-JFK flight. And S. Florida isn't all that much closer. Definitely not enough to justify a through flight on a F/J ticket for the partner.