My experience with
some, not all recent Toyota 4 bangers(whether Japan built or Canada/USA) is that when they are new they are very tight and have been known to idle VERY rough. I feel the valvetrain is partially responsible and requires additional breakin.
After a good breakin , as much as 3-4 thousand miles, it
suddenly disappears.
I have seen this in the last 4 years of engine production runs mostly on 4s but did see this one Sienna V-6 2004. The rough idle just disappears after breakin.
Tip= I would change the filter/oil with dino oil at 1,500K miles, not synthetic, and continue breakin with fresh oil.
My personal pref is Mobil 1 After 2500-3,000k for all my past and present Toys. But do breakin with regular spec weight oil. H/L, Ltd. V-6=5W30
I even do dump O/E oil and filter at 400-500 hundred with regular oil and continue with it till stated above. The O/E fill looks so dam dirty at 400 miles. Metallic content is high and visible. I feel most of this substance is from the first 100 miles of the engine breakin, as documented in alot of tech studies.
I then keep my Oil/filter intervals at 5k,10k,15k, 20k,etc.
Remember to document with dealer now ,your issue. and feel secure that yu have the balance of drivetrain warranty to solve this if need be.
Try to just enjoy the ride.