Now you can try and rules layer around it "if you use your combat counter-spell dice vs combat spell A and your manipulation counter-spell dice vs manipulation spell B each foci only added its dice to 1 test." shenanigans but I think the RAI is pretty clear
It's not. Let me explain why not.
In SR4, Counterspelling was PER SPELL. No Spell Defense Pool you split. So each time you 'spell-defensed', it was with a completely-fresh pool.
In SR4, the no-adding-multiple-to-same-dicepool rule thus only applied to the same Counterspelling defense, and of course what the rule mostly exists for, namely no adding-tons-of-foci for one Spellcasting/Summoning/Binding attempt and no stacking Spell/Spirit+Power foci.
So the same Counterspelling Focus would apply its bonus on every counterspelling test of the right type.
Now Spell Defense has changed, but the restriction hasn't really changed. So whether the existing restrictions were kept in mind with the altered rules, we don't know. Heck, I asked for official clarification, if it was as easy as you claim it to be I'd have expected Aaron to give an official answer to it. If they had stated it's a dicepool, rather than a pool of dice, then it also would have been very clear. But they didn't, and no official answer has been given on what you claim is a very simple question.
As such, there is NO clear RAI on it. The rules changed, but the formulation of the restriction hasn't changed enough. As such, it's unclear how existing rules with existing RAI should apply to the new case. Doesn't matter how much you bold the words, this issue remains, and until the FAQ actually answers the question, there is no clear intent and you can't just go and blindly accuse everyone noting it of rule-lawyering. Rulelawyering is when you argue Power Foci raise your actual Magic attribute, not when you say it's unclear which is intended in this scenario.