The crucial part of the rules is "... and max 25% in total". The slicing into groups of 12 is only for large matches.
We had a big discussion some seasons ago about this rule with admin @Phoenix_Scorpion. I was in favour of a simpler rule (using, as you suggest, groups of 4), but there was no majority at that time.
Given the experience with the Adelaide vs Misurata case, we may change the rule for next season. But there is no rule change during the season. The current rule is in essence "maximum 25% in total".
Why don’t you change it next year to be 1 in every group of 4 joined. That’s more obvious and what you are doing. Not 3 in 12.