Nope. The EEC does adjust for the fuel pressure by doing exactly what you say, but I wouldn't say you get less power. Even at WOT, it uses adjustment tables that are built when at cruise. It's not a long time, either, that it takes to adjust.
You can get two advantages from adjusting your fuel pressure. The first is when your injectors aren't able to deliver enough fuel for the amount of air you're getting into the cylinders. Say you only have 24# injectors but you need 28# of fuel to meet your fuel requirements. Since the throughput ratings are based on 39psi, you can turn your pressure up to compensate. Just take your target output (28) and divide it by your current output (24) and then take that result and multiply it by 39. Set fuel pressure to 45.5 psi and you basically have 28# injectors.
You may also feel that the computer is running too rich at WOT. You can prevent this by cutting back on the pressure some to prevent the computer from being able to provide too much fuel. This is a little more questionable since the computer may protect the engine and start limiting power. I don't think that happens, though, since some people seem to get an improvement when they do it.
The only way to get away from the factory set air/fuel settings is with a chip, the SVO extender, or something like the Speedbrain.
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351W 89 Mustang GT Convertible