To me it looks like rain only has an effect on non-wilted flowers. So if you have no wilted flowers on a day when it rains, none will be wilted the next day. But I've had the beautiful ordinance for quite some time now, so I could very well be wrong.
Yes, rain water all your flowers, i try it one rainy day. I dont watered any of my flowers and the next day all of them are still there and not-wilted. I dont have the beautiful ordinance
Rain "waters" your flowers in that it revives wilted flowers. It will not give them the "sparkling" buff that makes them more likely to spawn new ones.
It rained in my town for the first time today and I can confirm that it revives the wilted ones, but adds no sparkles for hybrid breeding. At first I thought it added the sparkles as well since there were suddenly a few sparkling tulips around, but it turned out that this was just one of my villagers trolling and confusing me. XD