I do not see a problem.
If someone tells me 'implement a 20% reduction of magic resitance" I will multiply the MR by .80
If someone tells me 'decrease the magic resistance by 20' I will subtract' 20.
Combine the two, and you get an effective -16. Just what it says on the tin.
Given that the chance to resist a spell is (100 + targetResistance - casterPenetration) / 100 is seems to me everything is fine.
If it looks wrong to you, it's because the two traits are subtly different, and you did not stop to consider the difference between them. On the other hand, if this many people are confused, I'd change it. Unclear rules are bad rules.