With the availability of the source code at Apple Open Source it is easy to see what happened.
| OS X Version | SmartcardCCID | CCID |
|---|---|---|
| 10.11 | SmartcardCCID-55008 | 1.4.14 |
| 10.11.1 | SmartcardCCID-55008 | 1.4.14 |
| 10.11.2 | SmartcardCCID-55008.20.1 | 1.4.20 |
| 10.11.3 | SmartcardCCID-55008.20.1 | 1.4.20 |
| 10.11.4 | SmartcardCCID-55008.40.1 | 1.4.21 |
| 10.11.5 | SmartcardCCID-55008.40.1 | 1.4.21 |
| 10.11.6 | SmartcardCCID-55008.40.1 | 1.4.21 |
I will try to closely follow the evolution of macOS Sierra (10.12) source code to avoid surprises in the future.