Meiklour, even dining on behest of the company is counted as duty time. Now I am sure you don't advocate skipping diner before an early flight!
The reason positioning flights count as duty is not because they are so specially tiring but because you are WORKING when you position.
A commuter is not working when he commutes. A commuter arranges his life voluntarily so that he chooses to fly to his work in his OWN SPARE TIME. So to come back to your question, a typical short haul commuter spends far less time traveling than most 'local' pilots who drive 30 to 45 minutes or up to an hour twice each day. And no, passing through security and boarding an aircraft is no big deal for a seasoned commuter. You just fast track through everything, you don't even think about it.
A quick calculation of a pilot who lives say, in AMS and works in LGW.
20 minute train ride to AMS, 90 minutes to reach the hotel in LGW, and then 5x ten minutes walk each day to reach the crew room, followed by another 110 minutes to come back home. That is a rough total of 270 minutes 'traveling', most of which is done reading a good book.
Compare that to a colleague who lives locally. 45 minutes to the car park by car, 20 minutes to reach the crew room by bus. Then again 65 minutes to go home after the duty. That is 130 minutes travel for just one day of work. Times five is 650 minutes every week traveling, most of which is behind the wheel of a car in busy traffic.
So are you sure that commuting is by definition more fatiguing?
I did not even mention that the commuting pilot gets 8 hours of uninterrupted sleep every day for five days compared to his local colleague who also has to run a family on those five working days.