I don't think all pops has is a shotgun. They deliberately went there to take out that t-800, so I'm betting they are holding back on just how they take him out of commission. I'm willing to give this a shot, but I'm also fully ready to admit that this movie was a bad move.
It's possible Sarah turns up with one of those cannons that we saw in one of the released scenes. She says ''Reese those bullets will kill him'' or something to that effect. Just, you'd have to wonder why they don't use this gun to start with, why they don't snipe the 1984 Terminator with it. Why risk a hand-to-hand battle that Pops could just as easily lose.
Oh, I don't consider the other soldier being canon either, but I do think the point of the original was that the time travelers were sent to random destinations, well, Reese anyway. He lands hard. In my mind, there was nothing to protect him from fusing to the environment (unlike the T2 spheres that melt anything in it's path for protection) and he could have very well arrived 30 feet in the air as opposed to just 8.
It makes the situation much more perilous for Reese and a risky plan for Connor and the Resistace. I like the idea that there's a risk that Kyle Reese could have been trapped inside a wall or fell to his death and be mistaken for a suicide jumper, leaving the Terminator, alone, with Sarah Connor in 1984. The original script, and even the final film has this feel of despair and treacherous dangers to it, from the rag tag future soldiers getting blown to bits to little kids playing/hunting rats, most likely to eat. I'd like to think that sending Reese and later, the reprogrammed T-800 (thanks to the events in T1) is a risky juncture. Knowing RIGHT where your soldier or machine is arriving kind of defeats that. I mean, LA is totally leveled. How would Skynet or the resistance remember the exact terrain and building locations from 45 years ago? I suppose Skynet could have files from developmental projects and maps from the past (assuming they weren't destroyed in the nuclear fire) but the resistance? They'd be taking shots in the dark. I guess Skynet, being an all thinking being might know where it sent the '84 T-800 and the T-1000 even though it was a last ditch effort, but I like to think that for Connor's technicians, they didn't fully understand the equipment they were using. For all they knew, Kyle might not even survive the trip. The original screenplay for T2 goes into all this, Connor even tells Reese to put his faith into the machine (the time travel equipment) because he's afraid to step out into the abyss.
I doubt Genisys dabbles in any of this. It's going to be a sterile and safe hollywood movie. They'll probably have exposition in the beginning that tells the audience that they're plugging in exact coordinates to the locations or Pops has files on everything from every point and time. Or hell, maybe not have a reason for any of it at all.
Well I'm not saying this is how it should be, only making a suggestion as to how Pops can possibly know where the '84 T-800 will arrive and where Reese will arrive. But as you say, they might not bother to explain it at all. What we can be quite sure of is that Pops has to come from the future war with this information, he can't learn it in the past. If they know in the future, then there logically has to be a way that they know - enter my suggestion.
On the matter of how would they know the exact layouts of cities that no longer exist...well there must be some remnants plus, as you said, some sort of records. Skynet probably more immediately has access to this information. The resistance, well some of them will remember, having been alive before the war. But otherwise they could find out or make educated guesses? Also, they might have had sufficient time to figure it all out. Even though the Terminator had already gone through they all still existed for some reason. Perhaps due to a BTTF-style delay of the changes in a timeline (OR the whole time travel plan is pointless and they just don't know it, not even Skynet - that other problem we've discussed before).