RAM had binary sizing for perfectly practical reasons. Nothing else did (until SSDs inherited RAM's architecture).
We apply it to all the wrong things mostly because the first home computers had nothing but RAM, so binary sizing was the only explanation that was ever needed. And 50 years later we're sticking to that story.
Just later, some marketing assholes thought they could better sell their hard drives when they lie about the size and weasel out of legal issues with redefining the units.
- magnetic media
- optical media
- radio waves
- time
There's good reasons for having power-of-2 sectors (they need to get loaded into RAM), but there's really no compelling reason to have a power-of-2 number of sectors. If you can fit 397 sectors, only putting in 256 is wasteful.
The choice would be effectively arbitrary, the number of actual bits or bytes is the same regardless of the multiplier that you use. But since it's for a computer, it makes sense to use units that are comparable (e.g. RAM and HD).