Don't name your game SC:Origins if the Origin isn't canon with the original.
Hopefully they at least keep close to canon.
By the looks of it Stardock dug themselves into a hole.
They buy the Star Control license for a quarter mil, so they have to make that back by making a game based on it. Not wanting to repeat Legend Entertainment's mistake with Star Control 3, they won't use the characters and races made by Toys for Bob without them, so obviously they try to bring them in. But *reasons* prevent that so they have to strike out on their own. Making a sequel seems out of the question, but a prequel... that could work.
So Stardock is making a Star Control game based on the notion that Mankind met space-faring races, in our part of the galaxy, before the Chenjesu arrived at Earth in 2112 and recruited them for the war against the Ur-Quan.
Then Toys for Bob become available for developing a Star Control game and Stardock is faced with a dilemma: Scrap their existing game and hand it over to TfB, or let them have a new title that they can work with from scratch. They chose the latter option, which is better for us Star Control fans, but leaves Stardock and the SC: Origins game in a bit of a pickle. Their only option is to go forward and hope for the best.
Making Origins lore work with Star Control lore is difficult, but not impossible. Off the top of my head, a rimward-bound deep space exploration mission for [PLOT REASON] is doable, as long as the end result is that Mankind either never learns about anything that took place during the mission, or that all information gained from the mission is kept Ultra Top Secret because [PLOT REASON #2]. Think the Water Chip quest from the original Fallout; the protagonist succeeds, but is banished from Vault 13 afterwards.
But hey, if we could stomach the narrative and story abuse of Star Control 3, we won't bat an eye over this! [/sarcasm]
EDIT: Missing word.