Would it be possible to give the 2 factions their own custom planets rather than taking established ones away from the independents? There are a few mods that already alter those planets and/or are dependent on them being independent.
I'm not sure if you're aware but 'historically' those two planets belong to those factions, nearly all 'minor factions' are lumped together as independents. Their planetary descriptions are untouched from vanilla.
I'm not aware of any issues related to splitting them from independents. As for conflicts other mods that interact with them, this is probably going to be a user-end issue. When I started KoC nobody (that I was aware of) was using those planets, the only conflict I was made aware of was with Iron Shell using Chitagupta in the Naraka which was promptly yielded. Now if somebody since has seen (or not seen) my KoC and decided they would like to get their hands on it and have a play that's on them.
Ok I did some digging around into where I was having some issues.
1. Ed Shipyards sell their ships out of independent markets of certain size (4 and above I believe) this loses Agreus as a market, but it's really a small issue in retrospect considering the number of other markets.
2. Industrial Evolution adds the Restoration Docks (Structure) and Salvage Yards (Industry) to Agreus, this isn't affected by your mod as such. It does however add more structures to the planet and the Salvage yards are pretty similar to your Shipbreaking Center, the Salvage Yards basically makes the addition of the Shipbreaking Centre and Heavy Industry redundant.
3. The removal of Tech Mining impacts the Terraforming and Station Construction a lot. That mod swaps the Tech Mining to Domain Archeology which produces a mod specific resource and is the sole initial exporter of said resource in the sector (Domain Era Artifacts) these exports are used to keep specific structures running around the sector (Like the Cryosanctum on Nomios) as well as for player useage.
I know more or less how to fix this for personal usage, but others might find it frustrating if they lack the know how.