The problem with their RP is: Why should it be more important than FDevs official storyline?
They made clever use of the BGS and justified it with their RP. FDev simply countered that action by manipulating the BGS in an absolutely legit way in terms of lore/RP.
The thing is that the 13th complains about FDev stomping over their RP, but fail to see that they tried to stomp over FDevs 'RP' in the first place.
The thing (from a RP-ers perspective) is that Frontier are the Gamesmaster. Their job is to build a rich tapestry which we, as players, can interact on. When things don't go their way, they should take it on the chin and move on, rather than moving the goalposts to suit what they want.
A clear example of what I mean is this:
Once we (as a group) were playing a pen and paper RP game, and came to a chasm that needed to be crossed.
My wife asked the question "How deep is it?"
Our friend (the GM) responded "40 Feet."
Our response to the obstacle was to get rope out of our backpacks, climb into the chasm and climb out on the other side.
It turned out, part of the 'story' he had planned was that we cut down a tree to make a makeshift bridge which would have angered some tree-loving creature, and lead to an encounter. Instead, he rolled with our decisions within the framework he'd built, accepted it and let the game play out the way we wanted (as the players).
By tinkering with the BGS to suit their 'story', what Frontier in the above example have done is effectively gone. "You reach into your backpack, and all your rope is rotten." or "You climb into the chasm. Rocks fall and kill the party."
That is what people are having a problem with.