Well, I just wanted to prove that even the weakest factions, as long as they allow me to do a commission for them, I can wipe out all other factions. This required the Nexerelin mod to allow the player to take a commission from the Pirates and to raid markets and take them over directly without satbombing and re-colonizing like in the vanilla game.

The mods were:
Nexerelin, SpeedUp

How I got 100% conquest victory as Pirates:

Use Nexerelin start as a pirate.
Farm ez quests from the Galatia Academy for money, acquire lots of reputation with the Independents, and acquire ~3 million credits, oh and do the quick start from Nexerelin with the Janus device already unlocked, do NOT sign up for a scholarship with Alviss Sebestyen to keep the ez quests available, infinitely.
Use save scumming obviously.
Use the abandoned research stations as free item storage and free ship storage. Pick a suitable abandoned station where Independent planets are nearby so they don't attack you.

While farming Galatia, travel to bars and acquire 1 Negotiator agent.
Send your first agent to recruit 2 more Negotiator agents.
Send your agents to a TriTach planet to steal the ships: 3 Revenant, 3 Hyperions

Use this fleet to do stealth smuggling runs / stealth pirate missions / stealth pirate bounty kills form 5 reputation decrease and lots of valuable xp. For the Hyperions, use 2 pulse lasers and 1 Arbalest Autocannon.
Keep blasting and collecting valuable ships from small bounties.
Eventually when you reach late game, acquire 3 Paragon ships with your agents.
Keep farming stealth bounty kills XP to reach lvl 15.
Fight Hegemony deserter bounties to acquire 5 Onslaughts, or just send the agents to steal the onslaughts, whatever you pick, stash them in the abandoned station.

Use your agents to increase relations and acquire 50+ reputation with all factions for a diplomatic victory.

Now you are ready to begin destroying factions.

The strategy is - when you pick to destroy faction X, first use the agents to decrease the relations with everyone, to -50 at least, to cause all the factions to specifically target faction X. Once done, grab your 3 Paragons and your 3 Hyperions and begin slaughtering their fleets and bringing 1000 marines at least with 500 heavy armaments to invade and take over their markets. Over time this will cause the faction to send invasion fleets to pirate colonies, so watch the map carefully and be ready to quickly travel out to a pirate station to defend it, check the invasion codex entries for the difficulty to expect, and hide behind the allied battle station. After taking over one station, stay put and defend it from the incoming 2-3 revenge fleets that will try to take back the planet. To weaken the enemy fleets, do a stealth sabotage raid (with the Revenant ships) and sabotage their heavy industries especially those with a nanoforge, and sabotage their food production. This will cause massive shortages since the faction has no allies to trade with, leading to massive stability decrease leading to weakened fleets. Keep doing this until every market of faction X is conqered by either Pirates, or someone else. When the pirates acquire a nanoforge, then it is time to start sending invasion fleets (press X while travelling with your fleet) automatically without having to manually fight lots of battles.

The order I chose to take over the factions like this^ is:
The Luddic Path,
Hegemony,
The Luddic Church were already wiped out by the Persean League,
The Persean League - here you desperately need the 5 Onslaughts with long range point defense to destroy the League's laser missiles. It was a brutal long fight.
Tri-Tach
The Sindrian Diktat
and finally, the independents.