After looking at the Microsoft.Web.Publishing.targets source, I have found a variable (ExcludeGeneratedDebugSymbol) being set to True in Release mode. From the comments, it looks like they wanted to exclude symbols from WebSite project, but the condition is not properly set for WebApplication project.
So, I have decided to override my build scrip from the caller arguments and it worked like a charm. I have not yet ascertained any side affects it may cause or using the undocumented property for future stability, but it works for now.
From the Microsoft.Web.Publishing.target file
True
True
False
I have updated my script as follows.