Has this changed since your post? I just did some analysis of Paint.NET 3.5.10 clipboard behavior and I can't get any real alpha data out of Paint.NET except in its proprietary format. Here's what I tried:
1) Create new 256x256 image in Paint.NET
2) Select all, delete
3) Set foreground color to white with alpha of 186 (0xBA)
4) Flood fill
5) Copy entire image to clipboard
6) Paste into my own .NET app
7) Call IDataObject.GetFormats(), IDataObject.GetData() on each format, and inspect the results:
"PaintDotNet.MaskedSurface" (MemoryStream, alpha set to 0xBA - clearly visible in the raw data)
"Format17" (MemoryStream, alpha set to 0xFF)
"Bitmap" (InteropBitmap, alpha set to 0xFF)
"System.Drawing.Bitmap" (System.Drawing.Bitmap, did not inspect)
"System.Windows.Media.Imaging.BitmapSource" (System.Windows.Media.Imaging.BitmapSource, alpha set to 0xFF)
"DeviceIndependentBitmap" (MemoryStream, alpha set to 0xFF)
I've also tested the following:
Copy from Word 2010 into my app: alpha is preserved (via "Bitmap" clipboard format)
Copy from Word 2010 into Inkscape: alpha is preserved
Copy from Paint.NET into Word 2010: alpha is lost (solid white background)
Copy from Paint.NET into Inkscape: alpha is lost (solid white background)
So, here are some possible theories:
Paint.NET is only intended to interoperate with itself when it comes to putting real alpha on the clipboard (suggested by my observations)
Paint.NET is supposed to put real alpha data on the clipboard in formats other than its own, but a bug is preventing it from doing so (suggested by your post)
My procedure is flawed (always possible)
Your clarification would be much appreciated.