Bro, if you have latest 1KR-FE, then in Vitz, it will be 2.8L with filter change and for Passo / Boon, it will be 3.1L with filter change.
Regarding manuals, I hardly think owners / users manuals and service manuals will ever conflict with each other. It does not seem logical to me and possible that in owners / users manual, the oil change capacity with filter change is 2.8L and in service manual, it is 3.4L.
100% agreed and I personally believe, YES!
(otherwise, dipstick will seem useless and meaningless, if it can not depict exact oil level in engine)
I personally believe that the best method to measure exact engine oil level (based on its capacity) in the engine is; when car has been parked on a perfectly flat surface for a sufficient time and engine has not been used for a considerable time, and is cold. In easy words, you park your car on a horizontal surface at night, and in the morning when you are about to leave, do not start the engine. Just open the bonnet, take out the dipistick and check engine oil level.
If you poured 2.8L, or let's say a full 3L ZIC A+ 5w-20 bottle in your Vitz, with latest 1KR-FE, and it touches the max. / highest mark on the dipstick; rest assured your engine is perfectly safe and fine (and is not underfilled at all! How can it be if it touches the max. mark? Can it be? I think, not).
However, if you pour 3.4-3.6L engine oil, then it may touch the max. / highest mark, may even cross it, but overfilling? One can think himself.
I hope. It all helps. Thank you.