The fundamental problem is that there should be shippers within the scale of the PC trade game that would pay more than Cr1000/ton/jump for J-2, might be some willing to pay for J-3, and perhaps even for J-4. At the very least, there would be non-ship-owners who buy goods within the speculative trade minigame and want to get their goods to a destination before someone else does, or before they spoil. PCs can do that! Why wouldn't NPCs?
But, again, the rules don't allow for that. The rules do strongly suggest that pretty much anything not being shipped by a megacorp as part of their integrated supply chain would move by a series of Jump-1s because that is all that the market supports.
One might get lucky and find a Far Trader (or Far Fat Trader) going your way so you can slip in a few tons of your stuff cheap as "filler" around their speculative trading loads, but that's not reliable enough to build an enterprise around -- if you need Jump-2 and have to wait more than a week for it, you may as well have sent it as two legs of Jump-1 each. And there won't be a lot of J-2 capable traffic, let alone anything higher, in those size ranges, because nobody's paying them enough to do it.
And that's how you get per-parsec pricing. Which, coincidentally, makes J-2 viable and J-3 almost so.
I look at that as a feature set- you come up in your mercantile trade dodging it out with jump tapes and dreaming of the day you can actually run Generate and go where you will, maybe speculating in lower end commodity items you can afford just to claw your way to that point.
Then you bulk up, arm the ship possibly for those juicy mail runs, upgrade the software a bit, and save up to buy a ship outright. Without the mortgage monkey on your back, that new ship can have a custom-designed mix of passengers and cargo suited to the subsector you want to operate in, including longer jump to more profitable mixes of worlds.
Or go small shipping line fast with the subsidized merchants and work out a scheme of your own mix of ships that do ship speculation in a network of value.
Another factor that won't be quite as spreadsheet friendly to figure out is that originally the 1977 CT ship encounter tables had the more profitable A/B starports have more pirates. So an unarmed Trader would tend to eke out an existence on the periphery and have to work up armament and software PRIOR TO going to the high profit planets.
So to get to that point and have the edge of profitability, the game had the built-in money sink of combat and better computers/software in the millions- or risk homegrown software..
So, taking these rules out of context can undo the whole scheme and expose what looks like weird choices, when we aren't seeing the whole picture.
However, there are only so many sessions we can run and the full bootstrapping up mercantile style can take a LOT of time to do. Just remember the whole adventure biome when pulling out things like the computer software rules or using 1981 encounter tables.
Personally I'm inclined towards the jump multiplier 'fix', roll number of lots/passengers x jump number (either way, multiply number of dice rolled or roll the results normally and multiply them), AND per parsec. That gives you a progression to larger higher jump ships, likely custom designed for specific routes to support them. Fun part? They HAVE to run high profit high jumps, each little adventure side trip is costly.