My tankers can self jump and are under 12 000 tonnes, they currently zip along at 2000 km/s with NP engines. The entire stock of fuel on every planet in the NCC's space would barely fill two of those tankers...Earth has 10 ML, Faewald 15 ML, Forge 9 ML, Possidean 9 ML, Bifforst 13 ML, and Rossetta has 10 ML; total: 66 ML. That is probably a slight underestimate.
I find it humorous that you consider a 50,000 tonne ship "tiny." It is a differnt scale to what I consider "tiny" that is for sure. The largest ship the NCC has is 45 000 tonnes. They are currently building a military yard that can handle up to 12 000 tonne warships. The ships you have cost more (in critical galicite) than 3 smaller ships that can carry more and don't require a jump gate network. Their sole redeming feature is they are faster (by a factor of 2 or 3 depending on which version of my ships you compare to). But if I have more ships on the route then the speed of delivery is the same. Plus I'm not sure why it matters how fast something is delivered. For military sitatuations speed is critical but for most other reasons if it takes 3 months or 6 months to get a factory from earth to the colony what changes?
There are additional expenses associated with those ships: ship yards have to be bigger, the larger the ship yard the more it costs to do things like switch classes and so forth. The more population require to use it as well. Each refueling sucks an pretty substantial amount of fuel out of the farm. The Tribals and the Magazines draw down that sort of fuel...which makes them coming in to tank up "exciting" and one reason for a long time they were limited in what they did.
I've come out of a two decade long fuel crisis, and have dragged myself out of a galacite crisis and mostly out of my boronide crisis to face the fact that my main stay mineral production (the CMCs) will burn out in a few decades and I have that much time to set up a series of outsystem mines to feed the beast. I look at things from the point of view how much fuel do I need to get from A to B, if it takes longer but saves fuel then "takes longer" wins. If people find 500 km/s painfully slow...my first long range freighters did something like half that...what is that "mind boggling" slow?
Largely I think the difference is mostly due to different mission paramenters. My freighters and transports are intended to be first of all fuel efficient, and to be buildable with my existing yards. Speed is whatever I get. The tankers are designed to do rescue missions so speed is important as is self jump...tanker capacity is whatever survives the other requirements. My refinery ships and terraformers have a higher need for speed to reduce transit times so they have more engines as speed is considered valuable as it improves their time on station. The as yet unbuilt small priority freighter has again the goal of moving at "speed" -- it is still "painfully slow" at 900 km/s, but can self jump.
I'm not saying my ships are better, that is purely a subjective opinion anyway. I'm saying my ships do the same job with a lower investment in resources overall but at the cost of time. It is up to a player to decide, in my view at least, what is important to them: delivery speed, resource costs, whatever.