It's really not that difficult of a concept to grasp. Batteries have no golden "100% charged" level, nor any true "0% charged" level, regardless of how people like to think about them that way. They ain't gas tanks, with actual fixed, quantifiable capacities. If you charge them to a higher voltage (all other things being equal), they'll give you more energy per cycle, but won't last as long. Same thing if you discharge them to a lower level. If you overcharge or over-discharge them by a huge amount, you've killed them in a single cycle. If you're very gentle with them (as the Toyota Prius is with its battery pack), you can get 100s of thousands, maybe millions, of cycles out of them. You just have to decide where you want to be on the curve -- charge them higher and discharge them lower, your apparent "battery capacity" will be higher, but you'll have a shorter lifetime. Charge them less and discharge them less, you'll have less apparent "battery capacity", but longer life.
Originally, it seems that Zero decided their goal would be 2500 charge cycles for its battery pack lifetime, and they designed accordingly. But it's clear that the goalposts have moved several times. (Any engineer will recognize the "shooting at a moving target" phenomenon.)
What disappoints me is that as owners, we seem to have no say in any of this. My bike used to charge to 100%, which it would maintain as long as it was connected to power. Now, if I don't ride it on the weekend, it's at 97% when I get on it on Monday morning, even though it's been plugged in the whole time. Clearly the latest firmware doesn't trickle-charge the battery while it's plugged in, so I leave for work without a full charge. A while back we had rain for several days, and it was at 94% when I got on the morning after. I don't like that. I realize the change was made to extend battery life, but I'm happy with the original 2500-cycle spec, and would prefer to always have 100% charge maintained while the bike is plugged in.