What I remember is that the armor bonus is applied after finishing the research.
For example, if you get a +3% armor resistance bonus, you only have to design a 97% resistance in the armor, and afterwards its gets upped to 100%.
This means your alloys don't have to be exactly perfect to still get 200% resistance as you are only asking for 197% resistance, this effectively means you get a bonus to armor integrity. You can still get perfect 200% armor with alloys that are a point off.