Zirconium is added to low viscosity/fuel efficient oils (required in VW 508.00) primarily to ensure they are not used in a backward fashion, ie; VW 508.00 oil used in a VW502.00 speced engine, and cause damage since the 502.00 engine isn't designed for such a low viscosity oil. Zirconium is not a naturally occurring element found in UOAs and thus makes it useful as a "tracer" for inspection analysis. Also, Chevron has mentioned it's use (and other similar metals such as vanadium) as an additive to prevent LSPI, albeit in small amounts.
Now, the question is will any manufacturer use it as a tracer to verify proper oil use? Depends. How voracious will they be in going after a claim, especially in single loss cases, to drag out an investigation just to save the cost of an engine replacement? Again depends on several factors, one of the most important being owner loyalty. How apt is someone to purchase another vehicle from the same manufacturer, or much less recommend it to friends/family, if they get a bad taste in their mouth from a denied claim? Most won't take the risk and eat the cost as a price for keeping people happy. I personally have never heard of any manufacturer going to that extent to validate or deny a claim based on which oil was used. I don't say it wouldn't ever happen, but depending on your level of suspicion, it's use during warranty period is up to you.