Alright moving the include after did the trick, I get my code in the final nsi file, as below:

set(CPACK_NSIS_EXTRA_INSTALL_COMMANDS "
    PageEx directory
      DirVar PythonDir
    PageExEnd

CreateShortCut \\\"$DESKTOP\\\\${PROJECT_NAME}.lnk\\\" \\\"$INSTDIR\\\\built_egg\\\\run.exe\\\" \"$PythonDir\\\\pythonw.exe\" \"\" \"\" \".$INSTDIR\" \"Run project ${PROJECT_NAME}\"
")


The problem is that it fails for this reason:
Error: command PageEx not valid in Section

which makes sense, but is there a way to avoid that PageEx to end up in a section at all?
Is that the only way to inject NSIS code?

At worst is there a way to just create my own .nsi file and use it directly?
I need to create a page which simply asks for a directory to the user, and then use that to create
a shortcut..

Any idea (also other solutions might be fine).
--

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