Olhando para a lista de valores SMART em Wikipédia , não encontrei nenhum valor afetado por Power Gestão e que você não listou.
No entanto, gostaria de acrescentar que apenas Contagem de repetição de rotação está marcada como "Vital", o que significa que todos os outros valores são apenas informativos.
O que é notável é que os valores de Contagem de Início / Parada e Contagem de Ciclo de Energia serão diferentes com o Gerenciamento de Energia ativado (como você suspeitava):
The difference between Start/Stop Count and Power Cycle Count is based on embedded controller and spindle. Single power-on increases both values by 1 (hard disk controller and spindle have been started), but after this operation Power Cycle Count will not change until hard disk power-off and next power-on.
However, while being in power-on state hard disk can go into sleep mode, which slows down a spindle. After returning from sleep mode to normal work, spindle is running again and Start/Stop Count attribute increases by 1 (second time). This situation is specially noticable while using ACPI/APM (Advanced Configuration and Power Interface / Advanced Power Management).
At the other hand, when you turn-off computer, hard disk controller automatically changes it's state to 0, but it takes a little bit of time for spindle to slow down. If you power-on hard disk quickly (before spindle goes completely down) Power Cycle Count will increase, but Start/Stop Count don't (as spindle is still working and it doesn't had a full cycle). One full cycle means a single change of state from 0 to 1 (off -> on).
Fonte: link (também vinculado ao artigo da Wikipedia).