What happens with SN+M&M and UX+FB is certainly that these programs are more financial products than loyalty programs. As with most financial products, there are high fees for all stakeholders (fuel surcharge for us), profits are taken and decisions are made by the strongest stakeholders = AF KL or LH. So smaller airlines don't benefit much from being part of the program as such. If they run their own program, they can make favorable arbitrage for themselves, balancing financial gain and increasing loyalty. Being part of an alliance allow them to still count on cross alliance connecting traffic and sales, and to provide alliance wide benefits.
Now will advanced emergency exists assignment still be free for FB Platinum members? That is the question, it was for me the main benefit of flying UX as FB Plat.