I have played guitar for more than 30 years and have played dozens of them. They all sound very different when played acoustically--each having its own distinct character. You can hear various aspects of their construction resonating and creating overtones and harmonics, and each design does it differently. Plugging them into an amplifier diminishes those differences to some degree. The microphone then becomes the great equalizer. When recorded, they sound slightly different, but major character differences are mostly erased as he demonstrated.
So, when recording, choose the a guitar with the pickup type you want (SC, HB, P90, etc.) that stays in tune, is comfortable to play, and has a scale length you can bend in tune.
My current collection. The workhorses are the bottom right HSS Strat and the top left HH Single Cut.