I disagree with the premise that exploration should be very logistically punishing, for two reasons:
1. Industry skills come with huge tradeoffs.
2. Punishingly difficult logistics simply isn't fun (for me) and I suspect for a large class of other players too.
What's fun about Starsector? Combat and finding cool loot are the two big draws for me. Doing spreadsheet calculations to see how far you can go and carefully shepherding your supplies simply isn't the sort of game I would prefer to play. Simply put, it feels like avoiding punishment, rather than seeking a fun reward. So your reward for doing the math right is just not dying when you go explore a new system? I mean maybe that's fun for some but it's not fun for me.
Okay, so even if you do find that fun, I think you can choose that playstyle. Just don't put any points in Industry. In the early game, if you put every point into Industry skills you're probably dodging combats and avoiding bounties and combat missions, because your combat stats will be gimped.
If a player wants to RP as a relatively peaceful explorer, avoiding combats and building up a strong fleet before respeccing into combat, I think that should be fine.
If the game DOES go the way you propose, I would hope that it comes with a greatly improved UI / tools. For example, setting multiple waypoints in a chain and seeing the total travel time and supply / fuel expenditure at base burn level and so forth. I understand that some people like that excel spreadsheet style of play, but I don't. I'm happy to spend a couple points in Industry in the early game to simply not have to deal with that, and feel free to travel.
Now one thing I can agree with is putting more combat threats at the edges of the map. The challenge of exploration, IMHO, shouldn't be running out of supplies. That just makes the universe feel emptier and more desolate. I would prefer that you find more STUFF in remote systems - more fights, more difficult enemies, more weirdness.
The most annoying thing about exploration is simply going to a system to survey it and finding NOTHING there. No habitable worlds, no probes, no domain security systems, no [REDACTED]. Just a boring, empty dead system. Put a boss fight there or maybe even just a paragraph of story scrap, a teaser of how the Domain used to be. The game setting is the ruins of a post-apocalyptic millennia-spanning galactic empire. Stories, mysteries, strangeness should abound in every corner of the galaxy.