We went through this when we bought our Sienna.
On the 04, it came with "regular" windows if you bought the CE 7 passenger, step up to a CE 8 passenger ($1,000 more) then you got factory tinted windows from the rear doors back.
We bought the CE 7 passenger and had the dealer tint them (they farmed out to some one in Kamloops) as we did not want 8 passenger and did not want to go for the LE at $5,000 more.
So could be either but I would think that on a newer mid to high end model the tint is factory.
Now the question becomes, is the factory tint in the glass itself or applied as a film as part of the process?