First solution: Yes, finding the PC CD for this game took me like 20 minutes, both new/old in even my country for something like 20 EUR. If the author wanted to, I'm sure they could have found it equally easy.

Second solution: Not really, when you do CD releases you have a "gold master" which is the final burned CD that the other CDs are copied from. That's the one you use as the official one, as that's the one most people on PC actually have.

If the game had multiple regions (something PC games usually don't), you have multiple executables. But this happens mostly for console games, but again wouldn't be difficult to acquire a specific one for one of the ~4/5 regions there is.

Re third problem, you're probably right about this. But I'd still argue that verifying information after a finding would add more credence to the story itself and cement it better, it wouldn't take anything away from the story (unless it proved that there isn't actually any story).