Agreeing with John there, putting these six-digit items into quests or dedicated rumor missions that require deep space exploration would be cool, finding them in Penelope's Star isn't. Reduced RNG, and a higher sense of accomplishment while also putting that carrot more visibly in front of a player sounds like a good idea.
That being said, I would appreciate it if we could argue from personal opinion, rather than trying to blanket dissent with claims of "most players want this". Personally, I would want to skip some of the starting bits and rather go into the wild of the deep reaches of space relatively soon, so the frigate slog doesn't do much for me. Later on, I also prefer the strategizing and fleet management, while letting the officers handle the fighting. Anecdote for anecdote, I know of people who see it the same way; that line of argumentation is a bit fruitless.
Now, if I recall correctly, there are different start options and a difficulty toggle, too. Retooling the game to cater more to single ship frigate bouts would take away from the aspect of fleet and supply management, which seems vital to me. Colonies fund fleets, fleets defend colonies. Fundamentally, Starsector presents itself as a rags to riches story of a plucky captain making their way against the big factions and [REDACTED], with all the grandiose frontier expansion that entails. It never really struck me as a game that wants you to stay in the frigate forever; it's but a stepping stone. At that point, I could make the argument that the game isn't wrong, Imaginary just seems to want something from the game that it doesn't focus on.