On Windows, I'm getting absolute paths in the project (.vpj) file.
For me, the working directory is shown as relative, and stored in the project file as relative. In project.e, the doOK() function calls okDirectories() which converts to a relative path - by calling the "relative" function. I see no sign that the include paths are stored as relative, regardless of the O.S. / platform. The function _ProjectSet_IncludesList does no conversion and I don't see any conversion in project.e where _ProjectSet_IncludesList is called. Maybe it's different on your system.
In _parse_project_command, you can see %IR and %IN can be used for converting absolute to relative (%IR) and relative to absolute (%IN) which they do by calling _relative_includedirs and _absolute_includedirs respectively.
Graeme