As an example, https://fluidfreeride.com/blogs/news/can-you-ride-an-electric-scooter-in-the-rain says don’t ride in the rain, but the main reason isn’t the scooter, it’s your safety. Visibility, stopping distance, etc. These are all good reasons, and you should consider your safety very carefully. However, they explicitly say “All new Mantis have IPX5 ratings. Light rain and some lighter puddles should be ok.” They later warn “can seriously damage your e scooter as it might get fully submerged”, which is consistent with the IPX5 rating. I’d point out that this is true of most cars and buildings too - they’re fine in rain, but not okay to submerged.
As for warranties, it makes sense that water damage isn’t covered, since there’s no way for the company to tell if you went through deep puddles (submerging the deck). But if you stick to light rain, avoid puddles, and wipe the scooter down when you get inside (and assuming they rate the scooter accurately), then I would not expect there to be any issues. Still worth considering your safety when riding, though.