>In general, you can't be paid for the commute unless it's to an "unusual" location more than a certain distance from your assigned workplace.

There's nothing barring an employer from paying employees a "commute stipend". I think you probably read about what is taxable/nontaxable. It's probably taxable as income and that's the "can't", which isn't really a "can't" at all; it's more of a "won't because it's taxable".