Is it possible to make the 'show flash instead' an option per default rule meaning it will be flashing if rule A is detected and showing the good border (red for example) if rule B is detected, instead of all rules would flash when 'show flash instead' is selected on that spell.

Ah ye I was just wondering if it would be possible to add an easy way to change each rule highlight method for the default rules since those rules are mostly good enough instead of using custom rules.

You have full control over the highlight type through custom rules. The Spells & Items settings are bound to the action (the spell or item placed in the action button), not to auras .