I’d say that if preventing boss cheese requires turning off the most basic core gameplay mechanic that the game is built around, then the entire design of the boss fight needs to be thrown out and rethought. Boss fights should make use of basic gameplay mechanics, not conflict with them. It’s not like this would’ve been rocket science for the Starbound devs. Terraria does it right, building suitable boss arenas is a major part of that game (the golem being the only exception, and even then only the first time you fight it). They could’ve just copied that like they copied so many other things. The lead dev of Starbound was one half of the original two-man team that created Terraria before founding his own company, so I’m really not sure how he managed to screw this up. He of all people should’ve known better.

As for Starsector, I remember there was a back-and-forth between the players and the dev with respect to the solo playstyle. Some players liked to take a small, fast ship and just solo entire fleets by kiting them around, so the dev implemented combat readiness to put a stop to that, effectively putting a time limit on battles. Players responded by using larger ships with longer combat readiness and making them fast by stacking both speed-boosting hullmods (Unstable Injector and whatever the other one’s called), so the dev made those hullmods mutually exclusive. It’s become clear over the years that he simply doesn’t want players to be effective in the game in either combat or command capacity. He wants the game to be a tedious slog where you lose a chunk of your fleet in every battle without there being a damn thing you can do about it.

The fact that combat is only a small part of the game and is all about fleet composition rather than fleet control is kinda the problem, that’s what I’m talking about when I say the game didn’t fulfill the expectations that its early versions created. Starfarer (as it was known back then before some copyright dispute) started out as just a list of battle scenarios, with no overworld map at all. It was all about ship and fleet control, fleet composition didn’t play a role at all because you couldn’t adjust it, you had to win each battle with whatever fleet the scenario gave you. Combat is the core of the game that everything else was built around. Unfortunately subsequent development saw basically no improvements to combat. Just about the only change I’d classify as an improvement was the command rework; in early versions you couldn’t even tell your ships where to move. Instead, the dev added more and more padding between battles, diluting the game to the point where combat is only a small part of it and is mostly decided by fleet composition rather than the player’s piloting and tactics. The game has become the opposite of what it promised ten years ago.