The "official" descriptions for parts sometimes aren't very meaningful. The term "Mayday" is used for some Toyota models to describe the telematics roof top antenna which seems like an odd term to use unless you're a pilot. I think the fact that the pre-2018 non-Limited Sienna with navigation had only a small satellite radio antenna on the roof, if they had a roof top antenna at all, is confirmation that the navigation system antenna is not in the shark fin antenna. The shark fin antenna was added to all 2018-up Sienna only when Safety Connect became standard on all trims. Prior to 2018, only the Limited had the shark fin antenna except in the early gen 3 model years in which Safety Connect was optional on the XLE.
As I said, I am certain that the navigation antenna for older Lexus models was in the dashboard - just under the top surface at the center. And I am certain that the roof top antenna on our Prius does not contain the navigation system antenna - I've seen discussions on what each "chip" in the rooftop antenna is for.
I've forgotten more than I remember about the chipset improvements that made it possible for GPS receivers to function inside vehicles without needing external antennas. Older GPS devices sometimes took "forever" to acquire enough satellites to function. I've got an old large clunky hiking oriented GPS device that I sometimes had to wave high in the air like a maniac for 10 to 15 minutes to acquire enough satellite signals (minimum of three required for triangulation) on cloudy days or in hilly terrain. The GPS chipset integrated into a modern cell phone can perform the signal acquisition in a split second. If only our military had had this technology when the Germans attacked Pearl Harbor!