Yes, Cave Story+ theme is different, it is remastered. And whole game is a bit smoother and so on. Also just checked some piano songs which were also original (I even got them with EAC) and their frequency was low too. Just trust it or not, but some songs just don't have high frequencies even in their original form, so it is definitely not that much reliable. Idea was definitely not the worst, but the rule, in my opinion might be this to prevent some issues:
Audio file must be reasonable quality. Its bitrate should be between 128kbps and *something*kbps. There must not be any encoding error and audio spectrum must be compared with original or highest available quality music file in external program (for example Spek), if there is a big difference in frequencies, it most likely might be an encode error and you have to replace the mp3 with better quality.
We just cannot say: "This song has low frequencies thus it cannot be used, no matter the original is same and it is suppose to be like that", that would not make sense.
Also some Umineko songs seem to have lower frequencies and the higher quality just doesn't exist, so this definitely has to be consulted.