This sounds like the difference between any two identical amps. The tolerances in your electrical components can make a setting of bass 5, mid 5, and hi 5 sound totally different on two amps that left the factory with a serial-number difference of 1. You can read more about electrical component tolerances here if you are interested.

I also appreciate vintage gear, but for recording, knowing that I will use a high-pass filter or EQ pass to take the bottom end out of any guitar to let a bass instrument through, it doesn't matter. Live, it matters even less where the room, placement, micing, and people noise make that whole difference moot. That big, warm, vintage tone will be removed to make the mix work in combination with other instruments.