Must be some Mandela effect but I'm sure that Paint.net was supposed to replace mspaint when it was started.
It was supposed to be a third-party replacement, sure, but certainly not an official one. It started as a student project. It's just the prefix that tricks your brain to associate it with MS's own .NET branded applications.
Paint.NET wasn't Microsoft's, but was an independent app: https://en.wikipedia.org/wiki/Paint.NET