The thing is, there's too much synergy between Devilish/Stunning Strike and the Curse/Blessing spell. To the point where either Devilish/Stunning Strike without the spell/blessing is useless, or Devilish/Stunning Strike with the spell/blessing is overpowered. This effect scales similarly to the flawed "Fire Arrows" perk with an upgraded ballista, but without it.

I haven't noticed any imbalance in the combination of Devilish/Stunning Strike with the spell/blessing, but again, you have boosted the effects of Stunning Strike (originally only 10%) and Devilish Strike (up to 100%). If you reduce these again, they will likely only be somewhat effective when used with the spell/blessing, and will remain unpromising on their own.

On the other hand, Devilish Strike + Overseer, Blessing + Stunning Strike, Curse + Torturer work well in racial classes, are unavailable to magical factions, and don't cause any problems.

In your case, is it correct to single out magical factions? You have introduced new classes, and for example, the Academics also have the Alchemist combat class with a 30% chance of getting attack stats and 20% defense when casting spells at 10%, and the Leadership skill with a 20% chance (correction - Alchemist is perhaps not a combat class, but a semi-combat, semi-magical class, but again, considering the other factions, it can be confidently said that there are combat classes there).

SA is a very rare build; you need to find at least a Mastery Amulet for it. Therefore, it is unlikely that SA will be able to compete with ordinary perks; the Great Rune will be virtually mandatory in all 95% of cases without SA.

It should be taken into account that in the proposed option, you can only find a double rune by spending 5 levels, and with your pace of the game, this is not a small amount (but again, it is definitely worth it).