The Zero battery brick uses 28 cells and the BMS lets each cell charge to 4.15V when connected to the charger (and Zero bikes have anywhere from 1 to 5 bricks in parallel depending on the model). 4.15V x 28 cells = 116.2V fully charged. If each cell is charged to 4.17V then you go up to 116.76. It would take extreme circumstances to be able to immediately regen 0.56V into the battery while at "100%". The max voltage you can charge a lithium cell to varies depending on the exact chemistry. Some chemistry can go up to 4.3V or 4.4V but in general 4.2V is a safe voltage that still allows ~400-600 charge cycles. At 4.1V you might be looking at ~800-1000 charge cycles. The higher the battery is consistently charged the shorter the battery life. The engineer has to choose between giving you more range per charge or more charge cycles. If Zero wanted to consistently charge to 4.2V they would hypothetically have to cut the 100K mile warranty to say 75K mile warranty. If they only charged to 4.05V maybe they could offer a 200K mile warranty. For a car you probably go for 4.05V. For a motorcycle 4.15V makes a lot more sense.
The point being....when you are charging from the wall the BMS can keep things at a nice 4.15V and Zero can offer a 100K mile warranty. They can let regen take it a little above 4.15V and still keep the 100K warranty because even under extreme circumstances its not going to go that much higher than 4.15V per cell just from regen. I guess it just took Zero a little while of collecting data to feel comfortable enough with the batteries to actually do it and keep the 100K mile warranty.
I agree with @BrianTRice, the change is definitely not just concealing the problem. They are finally doing it right in my opinion.