Pairing command/magic counter with materia that's paired with other support materia will let that spell/attack counter with the additional effect.
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This mod is now included in Postscriptthree's Tweaks, a collection of my mods in one .iro file for convenience. It has a bunch of other stuff too, all configurable, so check it out.
Materia paired with a counter materia and another support materia will use that additional effect even while countering. For example, pairing Magic Counter+Fire and HP Absorb+Fire will result in counter fires that absorb HP.
This mod uses the 7th Heaven mod loader. It's a relatively small adjustment to the exe, so it shouldn't conflict with anything.