Well, a step-down converter is a DC-DC converter. If you can tolerate the variable input voltage then it's best to run it directly off the battery.
Applying regulated 3.3V directly to the Arduino 3.3V pin (for 3,3V Arduinos) is the right way to go. If I was really concerned about power consumption, I'd make a custom board without the original regulator. You don't know if it's going to back-feed a trickle.
I've purchased the good conformal coatings before. They offer features like "solder-through" which means you can just apply a soldering iron directly and the coating burns off harmlessly. Great for repairs and adjustments on your prototype. They smell/feel/look exactly like clear ladies' nail polish. Now I buy all my conformal coating in the makeup aisle. They perform exactly the same as the expensive stuff.