There are CGs in which Frontier clearly doesn't want to lose. Salvation's CGs which offered module bribes, the pro-Sirius pact one which provided 4(!) pre-engineered modules versus virtually nothing for going against it (ship/engineer unlocks).Since the end of the storyline is supposed to lead up to another one, and fdev already worked on said upcoming storyline in advance, it was clear that the end of the current one would be dictated by fdev to lead to the desired outcome.
The same is true for most, but not all of the community goals.
Those you can influence usually have small to absolutely no influence on the wider universe.
It´s really more the rule than the exception.
These are the CGs which I believe could really turn the story, otherwise they wouldn't bother rigging one side so heavily against the other - most folks will go for the shinies.