Simple commands which can manage shipments of MSP takes out nothing from the game, inversely it adds to it in my opinion.
I did Orbital Defences for all my colonies and like you said I always put them on orbits. But making all colonies aelf sufficent is out of question as this time you would need to manage mineral shipments. Nothing wrong building right fleets, producing enough MSP, mineral hunting and transfering them to a central production place but at least shipping MSP when needed can be tracked by automated commands of our supply fleets.
And why not military stations in deep space. Whole idea is built around that. Steve made it like that. When you put maintenance stations there, you don't use it to serve your main fleet which is essentially served by main colonies. You want to put some threatening weapons there as a strategic place.
Edit: And there are more than one reason to create colonies. Maybe it has alien outpost for research boost, maybe it's strategically important, maybe it's a chokepoint etc. You can not expect from all systems can cover the mineral needs to be self sufficient.