Though my observations are for the Linux AppImage, I assume the GUI for the Windows executable is the same there.
Extensions → OpenBabel → Optimize Geometry, or the short cut by Ctrl + Alt + o offers an optimization. Noteworthy is Extensions → OpenBabel → Configure Force Field for that one can elect one of multiple force fields (GAFF, or Ghemical, or MMFF94, MMFF94s, or UFF) how the optimization should proceed and exit early provided adjustable criteria are met.
I don’t recall if there once was a coordinate transformation menu in Avogadro to either translate, or rotate a molecule. Wouldn’t this matter as relative orientation in presence of at least one other molecule in the same model? Or do you want to rotate e.g., a trifluoromethyl group around the sigma bond of C (of the CF3 group) to C (of the molecular frame the CF3 group is attached to)?