I'd expect the battery charge estimation to be recalibrated to account for the reduced capacity, not the hardware being deliberately hobbled to hide it.
I heard the old batteries, when giving high current would depress voltage long enought to trigger the shutdown, plausibly long enough to mess up the processor if it didn't shut down, but could genuinely give a lower current for a long time, such that rounding the charge down to zero would be harmful. It's easy to argue it's better to keep the phone slower then just shut it down when it can't reliably go fast.
Aging or damaged batteries can have dramatic'ly different output curves than the system expects. What looks like x% to the system can be at the edge of a cliff on the curve, causing sudden shutdowns or power loss.