Only downside to stacking Output when your higher rank is the number of attempts you get in deminishing (You cap out) and most of the items your targeting are "Rare" so you will only ever get one at a time.

I personally stack perception due to gathering not being something you need to focus on once you know the 2-3 hit zones on the notch your on. Although it does seem that perception has a cap ~10% HQ rate, not sure if those Militia items would bump it up to 20% due to the description.