Encoding version or configuration on PCB
Off the top of my head, two easy solutions come to mind.


Have n lines attached to the GPIO of your microcontroller. Tie these high or low depending on your board version. This would give you \$2^n\$ board configuration options. This would use n pins on your microcontroller. Static current draw would be negligible.
Have an input to the microcontroller's ADC and use a voltage divider with different values depending on the board configuration. This would only use a single microcontroller pin. This has the disadvantage that there will be static current draw through the divider. It would also be prone to BOM errors, while the first suggestion is hard wired to the board.


Both of these suggestions do have a weakness in that the end user could easily alter them, say to open up "locked" features. This may not be a concern for you, but something to bear in mind.