I don't think requiring silk touch for the automation setup adds much. I suggest instead:

• (flawless) always degrade by 1 level
• (not flawless, silk touch) don't degrade
• (not flawless, not silk touch) degrade by 1 level

Would also allow you to get a bit cleaner operation of the auto-replacing, as the annihilation plane storage setup would be able to tell the difference between damaged and regular certus blocks