When I first read the starship economics, it was apparent that a Free Trader was not intended to be commercially viable as a freighter/liner in "passengers and freight." I presumed speculative trade was a given, that was why it was called a Free Trader, not a Free Freighter or some such. When you couple the starship economics with the trade system, then the only question really becomes whether the Free Trader can get enough seed money to start trading; once they start, if they get a good run between A/B starports, then there is no end of it.
The Fat Trader essentially has to be, to keep all trade out of this "path of least resistence." Larger lines, I assumed, ran a series of both freight/passengers and speculative cargo, with the flexibility to route cargo in different directions based on markets, and minimize losses between big trades.
The M for adventuring always seemed a bit problematic. The player could run the M to work speclative trade, waiting for the right cargo, then possibly "buying out" of the subsidy contract.
IMTU, the Cr 1,000/ton is essentially not just a price cap, but also a guarantee that less capitalized trading/commerce can piggyback with speculative trade by owner-operators. A licensed merchant that is not under charter has to accept legal freight and middle passengers to its next destination. Once a passenger or cargo is booked to a given destination, cargo must be accepted until an hour before announced departure. Flight plans are encouraged, but optional; filing one declares the destination, and opens the Free Trader up for cargos. A flight plan announces a departure, which must be a minimum of two hours from filing. Not filing one opens one up for excessive attention from imperial and customs authorities; usually, once a specualtive cargo is purchased, a "short fuse" flight plan is filed, and some cargos or passengers may rush aboard. Often, a specualtor will travel super cargo with his investment.
IMTU Certain speculative routes are clearly more advantageous, and draw attention from pirates, even with A and B starports; for each repetitive "loop" that a free trader does specualtive on a given route, roll 13+ on 2D6 for a piracy/highjacking attempt, +1 for each repeat of the route after 1 iteration, -Streetwise/2, +1 if Industrial to Non-industrial, +1 if an M class, -1 if Scout/Naval base in destination, -1 if Scout/Naval base in originating system, -1 if per filled triple turret or equivalent, +1 if cargo base price worth more than 5 MCr, and an additional +2 if cargo base price worth more than 20 MCr.