Auxiliary government is no defense against your tax base being destroyed by a couple of Novaliths, and it also weakens your trade network. Considering the very high cost of setting up starbases everywhere... yeah. It's not really an ideal solution. The TEC have planetary shields, which are a much more affordable method.
The whole thing is problematic though, two Novaliths can wipe out any planet not specifically set up with expensive stuff just to defend against it. Two Deliverance Engine hits are a mild annoyance unless the fleet shows up at the same time. The balance on these things is way off, on top of Novalith spam just being annoying and not fun. This is not Sins of an ICBM. 
Though as for the last capital standing victory, the Advent Loyalists are even worse. The Titan's ultimate has NO defense. Not even Aux government stops it. If it can get to your planet and there isn't a massive fleet already there, all it has to do is fly in, hit the ultimate, and leave. No defenses in the game can kill a level 6 Titan fast enough to stop that.