The biggest issue with thousands of passengers is that you will spend far longer loading and unloading people then you will to get to your destination.
This is an important point. If you've ever flown IRL, you know that planes are full of slow people holding up the line as they try to stuff their giant overstuffed back into the overhead bin, and that it's annoying waiting for the other 100 or so passengers to find their seat and sit down...something which should be easy.
Now, multiply that irritation and waiting by 4 times. You're exasperated and impatient. Multiply that by 10 times. Now you're really pissed. You want to punch a guy because he missed his seat and had to go in reverse. Ten times again. You're now screaming.
Seriously, how long would it take for 4,000 people to board a cramped starliner? Can you imagine being one fo the first coupel people seated and having to wait for FOUR THOUSAND other people to sit before you could even take off? Not to mention the insane line at customs when you arrive in Nepleslia or the UOC. I agree that the starliner idea is very useful to the setting, but this particular modal may be too large for its own good.
Similar logistics would apply to your ship. It is going from populated, industrialized worlds to other populated, industrialized worlds. Also realize that even a long trip is not going to go much over two hours with its FTL speed.
I agree; a ship this size wouldn't have a big enough demand/market to stop on lesser populated worlds, so it would basically be able to get fuel anywhere it made sense to land. You're going to spend hours unloading your passengers anyway, so you might as well refuel while you're waiting.
My suggestion: Add an aether generator or UOC type compressed helium systems and do away with the massive fuel tanks. Instead, use some of that area for standard starship cargo containers.
You may also want to have some sort of moving walkway system that automatically speeds people to their seats, and have the landing terminals segregate passengers by seat number and load them all in order to speed things up.