As far as I know, it’s not deprecated, they just warn you about issues with using it.
Due to how Roblox handles property listeners, setting properties after parenting an object can cause performance issues. It would be in your best interest to avoid using this method. For more information, see this thread
Thread being the one you’ve posted, aka this Source
As @Legoracer has already pointed out, it isn’t technically deprecated. Such a designation has a specific tag in the API dump. The old wiki (which itself is deprecated, mind you) was also edited in October 2016 with the strikethrough, though no API happened to officially deprecate the second argument. In addition, the method itself isn’t the cause of performance issues, but rather how it is often misused. There are still some cases in which using the second argument is acceptable (for instance, when creating an object inside another object which has yet to be made a descendant of the DataModel).