I understand what you are saying. You want to defend your planet without using some gimmick that doesn't make sense. I'm using Sins One as a comparison again. Aux Gov lore-wise doesn't prevent damage to the planet. It prevents you from losing control. Think about Vasari. In the lore, they govern their slaves/workers using orbital structures and force their will through bombardment. Aux gov for all three factions showcases this. We also must remember the game is still in development and is not even close to being as balanced as its parent game.
Starbases are meant to delay as long as possible. They carry extreme hulls and shields with low DPS; your mobile fleet carries lower hulls but higher DPS. In terms of cost per hull/dmg, your mobile fleet and starbase should even out. The difference is your starbase will live long enough for you to reinforce it with a smaller fleet and/or repairs.
Based on the counter system that isn't present in Sins II quite yet. Starbase armor type is module armor and deals medium-type dmg. In Sins I, you use Tec Orgovs and Advent starfish to counter starbases because they outrange starbases and buildings. Anti-module ships were the counter to starbases. Anti-module ships carry high DPS, low health, extreme range, and use Very Light armor type. Anti-medium does 100% damage to Very-Light Armor. Anti-Module does 200% dmg to Moduel Armor Type. But most of the time that doesn't matter because the starbase can't target the anti-module ships unless using Target uplink. I think a lot the concern here comes from the lack of a "ship-type counter-system".
Long-range frigates counter light frigates
Module cruisers counter Starbases
Heavy Cruisers Counter Long range frigates, capital ships, titans
Light frigates counter support cruisers and flak
Support cruiser Counter heavy cruisers
Carriers counter long-range frigates and bombers with fighters or Counter heavy cruisers, titans, and capships with bombers
Bomber counter starbases bases, too
Fighters can be used to stop bombers and do moderate dmg to support cruiser/module cruisers.
You should think of Starbase as your hefty stationary Defence that allows you to hold a planet while you fight elsewhere.
My thought on this topic would be to keep Starbases as an early-game(Tier 2) option but keep aux gov a mid-game(Tier 3) option.
Another big thing. I'm not sure if the starbases include jump degradation. That might be another issue. JD = 30% hull loss and 100% antimatter loss if leaving a system with a Starbase present.
Fun Fact: Starbase in Sins 1 when Entrenchment was released starbases were almost unkillable in the late game. Titans and other dmg bonuses were introduced in Sins Rebellion to counter beefy starbases such as planet for the planet(AL), savage thrill(TR), regen in Culture (AR), Fury of the Unity (AL), phase jump dmg boost(vL), Militia(TL), and 150% hull regen rate(VL).
Like the opening cinematic says it all. The factions made titans push heavy defenses aka unkillable starbases with aux gov. My headcanon is the reason they split is to give the game more diversity 6 factions instead of three.
Another thing to mention is that Sins 1 holds a system that is rarely talked about. The "Chance to hit system"
Heres link and chart for it by someone smarter than I lmao.