I might have misinterpreted the final scene of that comic. (Not my fault, reviews did it first!)

The X-Files: Conspiracy's ending is probably set in the timeline where the virus was unleashed, and the timeline being erased was the bad ending... which means that Hearts of Steel and the IDW TMNT (I checked, they connect to it) are, I guess, part of the main X-Files timeline? I guess The Crow could be too, but well, no story connections to any other Crow.
The X-Files: Conspiracy is set in 2014. I don't know the specifics of the S10 comic timeline, but I imagine it doesn't extend that far. Maybe it's in the S10 tv timeline.
Let's say it's the IDW Turtles though. That means that they travelled the multiverse to meet the Ghostbusters who happen to simply be native in their home universe. Awkward.
In any case, say you don't want to include TMNT comics, it'd be easy to just include Conspiracy without Transformers, Teenage Mutant Ninja Turtles or The Crow.