Something like the Invisible Hand would be cool as a recurring command ship as you say. I certainly prefer them to the donut ships which could be increased in scale and become the space factory/cloning facility/base I proposed
The thinking behind the donut ship was "make a bad guy ship but make them different from Star Destroyers". They've certainly achieved that! But in doing so have ended up looking more like immobile space stations than ships -which is perfect for my concept, however their intention was to have them be actual ships - the model has engines on the back and everything.