I run Dream PSU's and thermal pad replacements on all m DC's and they all run as cool as can be with their stock fans (single drop of mineral oil in the motor shaft makes them run like new)
You are correct the Noctua fan does have a higher airflow rating but the Dreamcast either doesn't seem to supply it with enough amps to achieve it even if the voltage ratings would suggest so... or the 3D printed fan shroud isn't as air tight (thus not as effective at getting all the hot air out of the vent as the original fan's shroud).
Either way just hold your hand next to the exhaust vent and feel the difference for yourself. Put ear plugs in if you have to so the noise output doesn't subconsciously skew your opinion. You don't need any fancy tools or advanced knowledge on electronics to see what I mean.
Its been commented on in this forum quite a bit but no one's made an actual thread about it. And also it has nothing to do with the PS2 modding scene..I don't even have a PS2