A couple of comments based on more than a decade DIYing on various BMWs....
1/ In every case I've replaced rotors at the same time as pads. Even if the bulk of the rotor is greater than minimum thickness there's usually a nasty wear lip on the edge, and life in the salt belt has started to corrode the edges, vents and internal areas (include the hub/wheel mating surfaces on the rotor hat if it isn't painted) to the point that it just makes sense. Using OES parts suppliers and DIY the parts cost is pretty reasonable.
2/ the wear limit is to be evaluated at the time of pad replacement, not continuously throughout the life. The min thickness is intended to last through a set of pads - technically. If min thickness is reached 50% of the way through the second set of pads you're still "good" and they won't explode. Again, most of my BMWs have had rotor prices around $80 each even in Canada, so I simply don't see a point in skimping.
3/ CBS doesn't "estimate your brake life" in any way. A mileage-based counter starts when it's reset and it carries a default value that BMW thinks is reasonable. The check control system is based on a sensor, but it doesn't "measure" anything. If your pads get below ~3-4mm the action of braking destroys the sensor and the CC light is tripped. I believe that the CBS system is programmed to re-evaluate it's estimate of remaining life if the sensor is actually tripped (i.e. if it thought you had 10k left and the sensor is tripped it will immediately lower to 3k or something). I haven't witnessed it, but read about it.
4/ After service and fresh parts your brakes will most likely feel a lot better, but they are also unlikely to feel "bad" now unless you never bleed your brake fluid. Degradation happens gradually and you simply don't notice. After a brake job what I generally notice most is that the rears do more braking and the car seems to stop faster with less nose dive.
5/ Especially if you live in the rust belts you can't always rely on check control or measuring the pad thickness without disassembly. On my E39 the rears still looked good but after 5 years or something on my second set I decided to change them. What I found is that the center area of the backing plate that is not visible when assembled had started to break down and flex significantly when applied instead of actually squeeze the rotors. The improvement afterwards was dramatic, obviously, since the rear brakes were doing something again.
6/ Always use OES parts. Try to get coated (like Zimmerman Coat-Z) or at least ensure that you've used a high temp primer on the hats prior to assembly.