Suppose there are two employees: Alice and Bob, who do the same job at the same factory. Alice has a 10 minute (20RT) commute, Bob commutes 35 minutes(70RT).
If you’re the owner of the factory, would you compensate them for their commutes? How would you do it?
Nobody’s transportation and time is going to cost less than €0.21 per kilometer, unless you’re riding a bicycle and view that activity as adding value.
For anyone else, it’s a lump sum kind of thing. You’re compensated for transportation, but you still probably want to live relatively close to your workplace because there is nothing to gain from living far away.
I’m sure you can defraud the Dutch tax office but they’ll fuck you over big time, and I’m not aware of any such thing going on.