This is my theory regarding Portal 2 and Halflife 2: Episode 3. I think the Portal may not only have been conceived within the Halflife 2 universe as reference, but a key component of the story itself.
In the Halflife 2 cannon we know the Borealis mysteriously disappeared and that it involved Apature scientists who made a critical error when competing with Black Mesa. It is mentioned in Episode 1/2 from a message sent via video from Judith Mossman's character. It explains that whatever is on the boat can either help or be used by the combine. In the ships schematics that can be found in the Episode 2 game files, we see Glados name within them.
In Halflife 2, we are given an indication in Halflife 2 that Gordon Freeman hasn't aged, perhaps alluding to a form of stasis. The Gman characters apparently has ability to manipulate time, this is indicated in several sequences during Halflife 2 and it's episodic content. In Episode 2 we are told of two warnings given by the Gmans character with the phrase prepare for unforeseen consequences given to Eli twice (one of which during the original Halflife which opened up a world to world portal) as well as Eli saying the more I think about it the more I think he's referring to the Borlalis i.e. not referring to getting killed... The Combine came to earth through a Portal and in Episode 1, the Combines Portal link to earth is closed. Logically in the story, the Combine need a Portal to succeed, a motivation. The link between time and portals is established in the main halflife 2 game. When Alyx Vance and your character, Gordon Freeman use the Combines teleportation device to escape in the later half of the game. They arrive, for what was them instantaneous, one week later.
Summed up
When the Borealis disappeared, it shifted in time to place in limbo back to it's current time due to events in Portal 2. Portal 2 will take place on the Borealis, concluding with the Borealis being returned out of that state of limbo to it's current time. The events in Portal 2 (whatever it is) play a key role in Halflife 2: Episode 3.