Meanwhile, the standard 5400RPM hard drive is exactly 0% faster than the one in an 1999 iMac.
This is nowhere near true. The original entry level 1998 iMac HD was 4GB. The current entry level HD is 500GB. I'll have to make some guesses, but let's say that both drives were single platter (more likely today than in 1998). The speed at which you can read a platter is limited by the mechanics (rotation speed, track stepping rate x tracks count). I'd expect a higher track count over the years, but that might be offset by increased track stepping rate. The increased bit density goes entirely to speed. If you can pack 125x more bits/track, you should see the data go 125x faster at the same RPM.
Someone else mentioned that HD cache sizes have increased considerably over the years as well. So, I reckon that a modern 5400RPM 500GB drive is far faster than an old 5400RPM 4GB drive. Probably not 125x faster, but certainly not 0% faster.