I think that design is a cool way to do things- but for Starsector, I would worry about exploration. A decent chunk of the game is just wandering, looking for domain-era stuff.
Yeah, I'm not saying one design or the other is inherently better, and maybe (probably?) Starsector is meant to be a themepark.
There are ways to incorporate exploration into games with clocks though. Ultimately, exploration is trading time for resources. If those resources increase your power enough, it will be worth it even though enemies also leveled up in the time you spent exploring. This would arguably make exploration even more fun, because you would have to think about efficiency, hunt for breadcrumb intel to know where to search, consider burn level, sleapstream usage, etc. Right now, it doesn't matter if you spend 2 cycles to scout the sector, or 20. Nothing happens in that time anyway, there's no incentive to be smart or efficient.