Right, yes. I meant, I highly doubt that the auto would "keep up" with a manual, but I don't think it would be such a huge difference either, as you rightfully pointed out.
That doesn't matter, because, you have the 4 speed auto, and you seem to enjoy the car. This is what matters. I am 25 now. When I was 16, I bought a 1.6L protege with the 5 speed manual. It was a fantastic car to drive, especially as someone brand new to driving manual.
Based on your username, I am assuming that you are 18. You also seem to know about cars, pointing out shift points and what not. While I don't know anything about line pressure, the TCU primarily adjusts to maintain emissions and engine protection as priority over performance. All it really knows is, "the driver is applying conservative, moderate, or aggressive throttle input", and probably won't deviate much from the shift points it has learned from the factory. If conditions are not favorable for the throttle input you are requesting, such as, bad fuel, bad air, compromised engine health, that's the biggest reason why the computers would choose a different shift point. While it will adjust slightly if you're beating on the car, it's still going to be maintaining its factory shift points as priority, which is, try to cut timing and short shift on you, if it detects that you're not driving conservatively enough. That's the computers primary concern.
Assuming you are 18, I can tell you, that I too was 18 once, and beat on all my cars like a madman. I have learned to respect my current vehicle, the Mazda 6 as a transportation machine, which involves (usually) driving safely and conservatively. I too, hope you are one of the rare few who will mentally evolve into enjoying your vehicle safely and efficiently as time passes.
Enjoy your protege according to how it was tuned. It doesn't have much power in a straight line. Gearing in the 4 speed auto is not optimized. It does have a great chassis and suspension though, which luckily needs little power to enjoy. Go based on that.
Turbocharging your car as mentioned in another post is 1. pointless, because its a handling car, and 2. pointless, because it has a 4 speed auto. Learning to enjoy the car within its handling limits, which are high, provided you do a reality check with your expectations on straight line speed and focus on enjoying the great handling instead will keep you satisfied with what you have in present.
be safe and efficient. cheers