I hear what you're saying, for sure. The counter-point is that the game's focus is combat, and campaign-level activities should (generally! not always) funnel the player towards that. A high degree of unprofitable and bad-for-self-preservation behavior is essentially a design requirement.
Don't mean to tell you how to design your game, but thought I'd voice my opinion on this.
I respectfully disagree that combat should be the focus (or, at least, the overwhelming focus the way that quote presents it as) of the game. To me, the game is at its best when it immerses you in the world as a small business owner with a home port, small fleet, jobs to take and mouths to feed. The "fun" of the game, in my opinion, comes more from "how can I stay afloat with what I got" than "woohoo let's blow up another pirate fleet". The front page of fractal softworks seems to reflect that at least to some extent:
Starsector is an in-development open-world single-player space-combat, roleplaying, exploration, and economic game. You take the role of a space captain seeking fortune and glory however your choose.
I would also argue that, even if the game is meant to funnel the player into combat, it does not follow that "a high degree of unprofitable and bad-for-self-preservation behavior is essentially a design requirement".
Combat, in my opinion, is at its most exciting when the outcome is in doubt. Frequently, I see my fleet of something like 2 destroyers and 2 frigates being attacked by 3 (D) frigates. Without the ability to auto-resolve, this does begin to grate. Even if the game is meant to funnel players into combat, I argue there should be a distinction between "fun, exciting combat" and mop-up chore. There are two arguments against this that I can think of, I will try to represent them the best I can and address them below:
The first argument is that the CR consumption more or less deals with that. I argue it does not. I regularly play on 2x - 3x supply cost and, in mid/late game (3-4 cruisers and assorted support vessels) supplies cease to become an issue.
The second argument is that it's difficult to distinguish between fun, exciting battles and chore ones. This is a little more nuanced and I'll wall-of-text my response below:
I understand this point, I am a fairly adept player at this game (it's been what, 6 years since I bought it now?) and a painfully easy fight to me may not be so for other players. This, I suppose, stems from the fact that the game doesn't really have a difficulty setting (other than the easy mode, which I don't think is discussed very much and I can't comment on because I don't use).
I propose maybe a more involved difficulty setting can help with this whereby in higher difficulties, enemy fleets take you more seriously and won't engage unless they have at least even strength (or in really high settings, when they outnumber you significantly).
In the alternative, I propose an internal "player threat" tracker - a variable that more or less represents how skilled of a commander the player is reputed to be. AI fleets would (subject to some variability) only engage when their fleet strength is roughly equal or greater than the variable times the player's fleet strength, where fleet strength is estimated from ship size, quality, weapon quality, damage, and officers. So for example, the variable may start out at 0.8 (player has a reputation as a noob) and pirates may try to take on a player fleet of 2DD 2FF with 2DD 1FF with 1 d-mod. When the player beats that, the game will calculate the damage he took and readjust based on it. If the player lost 1FF, for example, the variable will remain the same; if he lost 1FF and had heavy damage to 1DD, the variable may decrease to 0.75; if he wiped the floor with the fleet and barely took damage, the variable may increase to say 1 and the next time enemies may be more cautious in engaging them.
Bigger fights would be weighed more than smaller fights, to prevent players from losing threat by feeding small fleets and then go marauding with a large one.
Hopefully that wouldn't be too difficult to implement. I feel it would add a good deal of dynamic difficulty to the game and keep funneling the player to battle without making enemies too easy and suicidal.