well in a "universe sandbox" capturing stuff is part of the sandbox.
but this has a story and the other factions are part of that so if you say start early game oblitering all the factions kinda breaks the idea that you violated the laws of the galaxy and everyone is out to get you if everyone is dead and piraterrs are almost as big a pita as the factions themselves being able to summon broken fleets.
and we can already depopulate and populate a planet and the only thing now is the stupid decivilized debuff pretty much negates the bonus of taking a core world, BUT as far as i understand it he intends to add a mechanic to remove decivilized, should just simply be paying to stabilize a place should do that, but the whole notion of "decivilized" and wtf is exactly going on is murky to begin with.
atm mods add the ability to raid stuff directly but its too easy, defenders should have a heavy modifier by default (home court advantage) and core and major worlds should have marines in the 1000s to bypass to take a colony. leveled up 1k marines will take out most planets in the modded game nm how much ground def they got. gives more a reason to level up that space and ground action skill though.
Either way the core game is going to have ways to take out colonies and recover them soon. so there is no real reason to rule out being able to do so more pro actively. embargos, attack, bribery, funding terrorists, there should be a variety of ways to wear down a colony and topple it, and most if it should be required before you work up to a military attack on any world that is larger than say 5. minor worlds just toss marines at the problem early on. and unrest being a thing when you take over an enemy factions place should be a thing, as well as a option for genocide and resetting a good chunk of the planets population.
If they could pull some of that off along with honest to god diplomacy and decent faction AI, there would not be such a "drive" to commit so much genocide. Tone down the invasions stuff, add ways to negotiate tariffs and etc on trade or breaks to buff your standing with a faction, and so on. lest with the diplomacy mods the yo yoing of standing is so schitzo it hard to keep track and with every faction doing stuff, stuff get lost in the shuffle less your checking intel constantly, better UIs could help there or notification systems maybe.
But it is the limited interaction with factions and the AI is what pushes some of the genocide and taking over the universe stuff. need to be able to interact with them beyond we invade you if you do too well. and that is it you cant say tell flat out you invade me i will murder you. or offer some concessions in trade deals to smooth their anger with your success. vs raid, raid raids, got enough colonies your being raided all the time by everyone.
if it is a sandbox give us more sandbox not less conquest is part of that.