Populated space is clustered in the middle, while explorable space is surrounding it and is at quite some distance. So you need pretty small fleet with tanker and freighter, otherwise you'd be suffering serious losses in terms of income if you run giant battle armada. But particular fleet built for exploration stands no chance in combat, especially if you got jumped by something big and scary, since you can't run away from everything, even on sustain burn, thus it means high risk venture. And definitely one you can't get into fresh from the start, while later it gets pointless.
This is absolutely not true. I can very easily turn a large profit with 5-6 cruisers and many supporting destroyers and frigates in my fleet. With the skills that give extra salvage/fuel, you can almost sustain indefinitely in the uncivilized area, but even without, you can easily stay out long enough to find juicy class IV and V planets that will pay out as well as bounties. Usually I come home because my cargo holds are full, not because I run out of fuel. Capital ships are too fuel hungry to be sustainable though, but the only thing you need a capital for is the remnant stations or large bounties, and you can specifically plan an expedition to deal with those things, you won't accidentally have to fight them. By super late game, I just lug capitals around anyway because I have enough money where I don't care.
Since the game presents no win condition, there is no true goal, only what you want. If your goal is only to have the most powerful flagship possible, then yeah, it doesn't make sense to take QOL skills that weaken you. However, My goal is to defeat my enemies, and have fun, so as long as I can build a fleet to defeat any enemy and my personal role in the fleet is fun, I've achieved my goals. I don't compare my ship to my allies, but rather to my enemies. As long as I have the potential to beat them, I'm happy. I'd rather have more powerful enemies than myself since it presents a challenge. Having an OP flagship that murders everything without difficulty is boring for me. (but I can understand that other people do enjoy that)
I've found that both exploration play throughs and combat play throughs can satisfy my goals. I personally enjoy exploration and finding exciting things in the unknown, but I can see how if you didn't enjoy that, the whole play style would seem unappealing. I think people who don't enjoy exploration by itself have probably never committed to it enough to see how reliable, safe and profitable it really is. It's fine if you don't want to play the game that way, but that doesn't mean it isn't possible or enjoyable for someone else.
Ultimately, it's up to Alex to decide what he wants to be possible in the game and what he wants the win conditions (if any) to be. Optimally, he would make all play styles viable, but I don't think that is realistic.