I imagine that there is a small but measurable impact on fuel economy at speed.
Possibly aesthetics (designers can be prima donnas) when not needed.
The oem feet/bars are a neater solution & possibly more secure solution when they are needed with no chance of marking of the roof, albeit twice the price than 3rd party.
Again, not a Toyota only thing - Audi, BMW, Ford, Vauxhall etc. The Mazda 6 Tourer seems to be 1 of the few still with a traditional roof rail as standard depending upon grade (i.e. you are paying for it as part of the grade) - the base grade doesn't have rails.