Personally, I think they didn't include a map for the large cities on purpose, and that it's actually one of the best decisions they've made in a BGS game since Morrowind. I also don't expect anyone to agree with me, but that's fine.
What I've been trying to figure out is why the gameplay loop in this game is so smooth and why I haven't gotten burned out yet at all. I think it's because of this decision to not include city maps. It's a subtle, but significant distinction. That switch from following a checkpoint for large parts of the game, to using the galaxy map and trying to remember systems and planet layouts, to then returning to large cities and relying on memory and spatial awareness I think is the main loop that keeps it all going and keeps it from feeling like work to me, like so many other open world games that aren't half this large or demanding.
At the risk of over-explaining the obvious, I think it's the main thing that has elevated immersion in this world for me, and one of the main things that elevates the side quest discovery. Out in space you have segmented travel using a scanner or galaxy map, picking a landing spot or fast traveling. Then when you return to the city, you switch to the loop of it feeling like your neighborhood you're familiar with since you are forced to rely on memory instead. It reminds me of the Hades gameplay loop of going through a randomized attack level, then returning to the comforting lair that you've customized and memorized every inch of. It recharges you somehow and then you feel the urge to get back out there again.
In countless open world games I couldn't tell you where a single thing is from memory. You click it on the map, follow the icon and end up where you're going. That works, and is necessary for a lot of quests but I think that doing nothing but this is what leads to open world burnout. In contrast, I could tell you from memory where 2 dozen landmarks and stores are in New Atlantis with directions to get there. That is a totally different experience that sticks with you far longer and results in a richer game. That's what "immersion" is - literally.
Personally, I think this is also what makes so much of the quest discovery feel special. You do have periods where you're searching for something and don't know where it is. You have a destination in your head but you wander through 4 places you didn't intend to before you get there, and you have a big chance of finding a quest or two randomly before you even get there. That is part of the secret sauce as well. If you have a checkpoint on your map and you're just efficiently moving from A to B at all times, you're not mentally in the "exploration" mindset searching for something, you're in the worker mindset and may not even feel good when random quests pop up like that. I just found a quest last night in the UC Security Office right by the spaceport. I've ran past that 100x and didn't even know it was there. Then last night I finally walked up to the door to check kinda on accident and saw you could go in and there's a whole thing in there. That little dopamine hit of discovery is the whole point. The best example of this is The Well. It was probably one of the most enjoyable discoveries in the game to go down a seemingly unimportant elevator and realize there's basically a whole 2nd city hidden that you didn't even know was there. I'd be willing to bet that's when the game "clicks" for a lot of people too, because they get a big dopamine hit since they didn't know it was even there. It's the inverse of the Morrowind gameplay loop where you have maps for the city, but out in the wild you're following random directions from NPCs and using spatial awareness. Here, you have checkpoints in the wild and then spatial awareness at home. It's not an accident that this is the first game of theirs that made me feel like I did playing Morrowind.
My 2 cents anyway, I don't expect most people to agree. I think it's the kind of eccentric decision you'd only even get from a studio still lead by an auteur director. Otherwise it would just get vetoed by committee. I'm just glad Todd Howard is still actually directing, because we likely won't get many games like this.