On Windows, the manifest is indeed necessary for opacity to work. That's how the Windows API works. Actually how GDI+ is invoked as the default drawing API.
But a manifest resource can contain many more information, e.g. access rights.
So the manifest resource needs to be debugged.
I have not enough knowledge of SDL, if at all, I use OpenGL always directly or use Windows API's, but can you point me to the offending manifest?
I might be able to see where it goes wrong.
That is, unless SDL transparency clashes with the Windows transparency: that is almost unfixable.
The OpenGL API does not use high level native Windows drawing API's.(GDI and GDI+) It uses the graphics driver directly.
In the worst case, with OpenGL you would probably need a complete OpenGL drawn widget set, comparable to the custom drawn widget set to support consistent opacity for all controls.
That is, I see no technical reason why the Windows drawing API's would clash with OpenGL.
In effect all use the same low-level graphics drivers.