You are on the right track. Lipo -> boost -> arduino and other devices. You definitely want to connect the arduino through the +5V pin, not Vin. Vin leads to the on-board voltage regulator which needs at least 6V to operate and since you already have 5V from your booster, just use that. Connect all your other devices to the same pin.
As for a 0.01V variation, that is nothing. If you took the time to measure many of your 5V phone chargers, you would see much more variation than that. Anything within 10% is normal (4.5V to 5.5V)