Well, for one, there’s no place for them to fit into the story, they were introduced solely for multiplayer purposes and that is decommissioned while 47 is still playable in sniper. Ergo, the sniper missions are 47’s missions. The mobile Shadows game’s canonicity is questionable because of the timeline.
PZ takes place shortly after Club 27 because firstly, Diana tells 47 “Welcome back,” at the start of the mission, which she does not in any others that I recall, indicating that he was very recently just there. The suite where Cross’s crew were recording their album still has equipment there, but nobody doing anything, indicating the mood is somber. There is also an NPC in the wing of the hotel who mentions that Jordan had died that morning, indicating that 47 completed the first Bangkok mission that morning, left, Nabazov’s cult arrived and set up their stuff in the other suite for the rest of the day, and by night, 47 is back at the hotel for his new contract on them, which ties in to Diana’s greeting. They’ve set up fast because Ken Morgan was not going to be staying at his suite long, he just wanted to meet with Dexy and finish everything, so that covers why the cult is already prepared to set up their gallery so quickly.
The campaign takes place over the course of the next few days, about week, and so by the time they are done, the thing with Thomas Cross happens, and then nine days later Freedom Fighters, giving the militia enough time to tear down that tower 47 sniped their infected members from after they realized where they were shot from, hence it’s absence in FF, and gives GAMA time to put away all the stuff they had set up for Owen Cage by the time 47 gets there.
Most Paris and Sapienza ETs are fine as they take place pre-WoA (Dalia and Viktor likely hold shows and auctions every year), but no indication that they actually happened, and the Marrakesh ones are iffy, but possible I’d we assume that there was a different riot outside the embassy when Strandberg was first arrested after his scheme was exposed, and the one that happens later is a different riot that happens about a year later when he’s busted out. The Bookkeeper can’t be canon because it explicitly mentions the Shadow Client, but 47 was only ever in Colorado in relation to the Shadow Client in FF (the times in PZ and S6 were for different reasons and before they even knew what that militia there was about), and no indication that Grey kept his forces on that farm after 47 killed Rose and Co…
The Stowaway and the Appraiser can’t be canon because 47 only went to Isle of Sgail once, so they are out. The Revolutionary might be possible before WoA. The Undying may have happened since he’s later mentioned in Mendoza, but the Undying Returns is likely not canon because that would imply 47 failed, which he does not do, so that one was just for us players. While most of the H3 ETs may have happened, the Procurers is patently impossible, because of the death of Zachary Carlisle.