So, I somewhat read Matriculated but had never read Retail Rage around the time of the crossover. I read through the Retail Rage archives the other day and enjoyed it but it took me a while to put two and two together during the crossover. I was wondering why Janette was not getting any lines and then I thought, "Wait, Janette...Janette...I know I have seen that name somewhere before. Boy, she is awfully famili-Hey! WTF," and immediately ran over to Matriculated and connected the dots.
I would love to see another one of those even if it was confusing for me at the time. Unfortunately, like you said, this storyline crushes that possibility.