That's not how it works in real life. Before cars were smart enough to tune themselves the engine would get all out of whack as you added different parts. Something as simple as an intake and exhaust on an old Civic would ruin the engine's tune, resulting in rich smoke in the exhaust. That's what we're talking about.
That's not how it works in real life either, or at least, not universally.
I'm not sure how much the average person here knows about how engines work and are tuned, so I'm going to go through the 101 level of engines and tuning.
A car engine depends on two things to make the best power, all other things being equal: having the right amount of fuel in the combustion chamber when it fires, and triggering the spark at the right time.
The right amount of fuel in the combustion chamber for best power is generally considered to be ~12.5 x the amount of air by weight. This means that petrol must be precisely metered for the amount of air flowing into the engine. The original scheme for accomplishing this metering is the carburetor, which meters the fuel through mechanical means. The modern scheme is electronic fuel injection, which uses some kind of sensor suite coupled to a computer (called by various TLAs, an ECU in GT parlance) to deduce the amount of air going into the engine and direct the injectors to fire to provide a controlled amount of fuel. (In between there was mechanical fuel injection, which I know little about and shall not discuss further.)
The right time to trigger the spark varies with both the speed and the load on the engine. In general, triggering too soon will fire while the piston is still going up (not just bad for power, but likely to break something), while triggering too late will fire after the piston has already started going down (bad for power). As the speed of the engine increases, the spark needs to be triggered earlier to allow time for the combustion to progress through the cylinder. An example of this would be a late-80's Ford Mustang, which has base timing of ~12* before top dead center (BTDC) which is advanced to ~35* BTDC over ~3500 RPM (exact numbers may be different, but all are in the right ballpark).
The original scheme for altering timing was purely mechanical in the distributor, with a system of weights to handle advancing the timing and points producing the spark. By the mid-'80's, there were semi-mechanical systems where the weights and points were replaced by an electronic system controlled by the ECU but there was still a rotor for delivering spark to the plug wires (which would allow base timing to be changed by clocking the distributor body).
With electronic fuel injection, there are two major sensor suites and schemes for deducing the amount of air going into the engine. One of these is known as "speed-density" and the other is known as "mass air flow". With the speed-density scheme, the physical and flow characteristics of the engine are pre-determined, with the density of the charge air measured by a pressure sensor and temperature sensor on the intake. With a mass air flow scheme, the actual mass of air is determined by measuring atmospheric pressure, air temperature, and the volume of air passing through a sensor.
So, how does all of this relate to tuning?
While timing is somewhat important, it's usually set pretty well from the factory. With a mechanical or semi-mechanical system, you can do some things with timing, with a purely electronic system (coil on plug, etc), the only way to fool with the timing is to mess with the ECU.
The big issue is the fuel metering. Remember how I said a speed density system has the flow characteristics of the engine pre-determined? That means that pretty much anything that fools around with the engine is going to screw up its behavior---and offhand, I think it's more likely to end up lean (with more air going through than is supposed to be) than rich, which is very bad for the health of an engine when you're driving it hard. In
this case, your statement, "Something as simple as an intake and exhaust on an old Civic would ruin the engine's tune" is correct.
But you remember how I said that speed density isn't the only possible system for metering fuel in an engine? In a mass air scheme, the computer may have a fairly broad ability to deal with an engine that will move more air. It will depend on whether the air meter has the capacity to signal more air and whether the fuel injectors can move enough fuel (and even
that can be partly addressed by changing the fuel pressure regulator to get higher pressure on the fuel rail). In a mass air car, you can do a significant amount of tuning and see the engine take it in stride. An example of this that I'm relatively familiar with is the Ford 2.3L turbo four-cylinder engine from the mid-late '80's. As it shipped stock in a Thunderbird Turbo Coupe, this engine was spec'ed at 190 bhp at the crank in a manual transmission car. The stock air meter, fuel injectors, and ECU can handle ~250 rwhp---that's with things like a cone air filter, replacement exhaust, port-matching in the intake, maybe bumping the amount of boost,
but no tuning of the fuel or spark whatsoever, just the stock provided by the ECU.
Of course, that's also not getting into the issue that you don't want 12.5 AFR all the time, you will want higher for part-throttle and off-throttle for better fuel economy when you don't need max power, and you maybe even want higher for full throttle depending on whether you're normally-aspirated or boosted, and so on...
(And how do carbs fit into it? I'm not sure how well they typically deal with moving more air through the engine, but I do know that they need more fine-tuning than an ECU due to less capability to adjust to different atmospheric conditions, and they have a lot of latitude for aiming for a particular operating envelope by tweaking settings or internals.)
tl;dr: What kind of tuning is required for maximum performance depends on how extreme the modifications are you're making to the car, and how well-equipped the car was to handle modifications in stock form. Some can take a lot more power just with simple bolt-ons, some require modifying the ECU for even relatively minor changes, and carbs require different kinds of tuning altogether.
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