Yeah, pilots can still run out of gas, bucketing a 5 minute cycle until the low fuel light comes on, "one more" quick maintenance flight with low fuel, external load ops where you wait for real low fuel to pick a heavy load....and, as I said of long distances offshore you'll plan it pretty tight. I've bucked enough 60 knot headwinds to know its going to take more fuel, but those are a rarity and if they hadn't been forecast then all the fancy pencil work still wouldn't have saved you.
I'll say it again, ENG and EMS pilots never put a pencil line to a map for any short little trip of less than an hour. They never fill out a trip log with all the little boxes for CAS, TAS, Actual Wind, etc. Ever try filling one of those out while you're flying an Astar or Jetranger, with the cyclic in you knees?
You can rely on your GPS about as much as you rely on your tail-rotor. Both can quit but rarely do. If you end up going 90 degrees off your direction you are flying an illegal aircraft without a wet compass, or you've forgotten where the sun rises and sets. Gimme a break, even if it quits ten minutes after you've departed, you still have a heading and ETA good to within a couple of minutes. The rest is looking out the window.
I believe the original question was by a new pilot that was trying to resolve the detailed flight planning that he did in training with what is to be expected in the industry. My answer is that you don't do the same, you employ any number of shortcuts, but the principles learned from the planning exercises are what help give you the judgement to safely get to your destination and back on a day-to-day basis without the pencil work.
Malabo