Mod factions are difficult to balance and so when you toss several of them into a mod compilation, some are clearly more powerful than others. Ideally the discrepancies are minor and vary between ship types/tiers and strategy/how a ship is meant to be used, but often it's unbalanced across the board. It's really tempting while playtesting to bump up the stats to make your creations just a little more powerful than everything else, but if everyone is doing that you can see where the overpowered trend comes from. As David said in the blog, "If every ship was totally awesome then no ship would be totally awesome. Starsector needs standard “boring” workhorse ships."
I made a spreadsheet balance tool (BalanceSuite 5000) a while back that helped devs balance their factions to vanilla by showing them how a particular ship compared to others of its class and even recommending stats given its price, ordinance, etc. The idea was that it helped devs take a step back with, "Hey, that's overpowered for this type of ship and here's why, try this stat instead." I thought it was a pretty useful tool until a major game update broke it.
IFed is due for an overhaul where some rebalancing will take place. While I want it to play nice with other mods, it will only be officially supported as a standalone mod to use with vanilla.