Okay there is one issue that looks like it might be venv related, which is that upgrading pip itself doesn't seem to work for some reason (while installing other packages in the venv worked fine):

Could not install packages due to an EnvironmentError: [WinError 5] Access is denied: 'C:\\Users\\Jonas\\AppData\\Local\\Temp\\pip-uninstall-l4qh2ucu\\myproject\\tools\\windows\\.python-win\\spen-venv\\scripts\\pip.exe'
Consider using the `--user` option or check the permissions.

Traceback (most recent call last):
  File "C:\myproject\tools\windows\\windows-build.py", line 136, in <module>
    do_build()
  File "C:\myproject\tools\windows\\windows-build.py", line 74, in do_build
    os.path.dirname(__file__), ".python-win", "spen-venv"
  File "C:\myproject\tools\windows\.python-win\python\tools\Lib\subprocess.py", line 395, in check_output
    **kwargs).stdout
  File "C:\myproject\tools\windows\.python-win\python\tools\Lib\subprocess.py", line 487, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['C:\\myproject\\tools\\windows\\.python-win\\spen-venv\\Scripts\\pip', 'install', '--upgrade', 'pip']' returned non-zero exit status 1.
C:\myproject>

I would expect that to work even without --user so I'm not sure what is going on