AmpedRobot
You can set the version number x.0.0.0 in Construct's project properties (where you put your game name, window size, etc) and then you don't have to edit it in Visual Studio.
I don't know what Construct advertises, but playing PC games with Xbox 360 controllers was very common, it was pretty much the standard for years. Until this past year you couldn't even make Xbox games with Construct, so I guess everyone knew the 360 controller support was meant for PC.
Xbox 360 came out 12 years ago and is very old, no one is making games for it anymore, that's just how consoles go. I doubt many people turn on their Xbox 360 anymore, even if they still have it, so its current audience would be pretty small. And html5 games would run poorly on it anyway.
As for your other build and controller issues, they sound like regular Construct / game dev issues, so you should probably start a different thread elsewhere. I'm not too knowledgeable about those. I personally have not noticed differences between Xbox One and 360 controllers, but I haven't particularly tested for that.
If you are manually copying files from different builds or something, I would think that's very risky. But again I'm not knowledgeable enough about it.
For the newer NuGet packages, are you talking about the ones that end with XboxOneXDK? It seems those are used by people in ID@XBOX, but not for UWP and the Creators Program.