I'm pretty sure, not positive, that the main difference was how they were packaged. Original the IFU and CDROM2 were packaged separately to avoid a VAT on "audio products". This way you only paid the tax on the CDROM2, and not the IFU. Considering what this stuff cost back then and how crazy certain taxes are in Japan (%50 on VHS, for example) I would be surprised if this saved people ¥5000 or more.
Soon after the tax law changed. I'm not sure if it changed in a way that this trick didn't work any more or if it changed in some other way. Regardless, they started selling the CDROM2 and IFU together after that.
There are no functional differences.
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