Free traders are more akin to semi-trucks than the smallish freighters that ply the waterways of today. You'd have to go back to the early 1900s to really get into the tramp freighter model, where smallish freighters (in the 5k displacement ton class) plied the worlds oceans and carried the cargo everywhere. Norway, for example, had the fourth largest merchant fleet at the beginning of WW1, but by per capita it was the largest in the world.The cargo rules say that the final volume is "X". They say nothing about what form that "X" comes in. It could well be crates or barrels or bales or whatever. That's why that stuff is what's called "general cargo".
Fine. You win. Shippers are absolutely constantly sending lots of containers to non-container ports where they can't be processed and will forever be out of the system. I don't know where you got the idea I said that no one ever disposed of excess containers. I was explicitly talking about trading with backwaters not designed for container shipping and where there was no chance of those containers going back into circulation.
Yes and no. E class ports are absolutely not possessing facilities of any meaningful sort. Class D ports are subject to the usual Traveller ambiguity. They might be a largely abandoned large port, they might reflect a substantial private commercial port with only dregs available to public and non commercial vessels, or they might be just an airport with a water tank to refuel starships. The vast majority of Class D starports have no orbital capacity at all, so they are only designed to handle small ships. Most of them are also in worlds with negative importance, so they are probably not handling very many ships in a given week if you use the WBH or T5 charts for that sort of thing.
Containerized shipping in the commercial/logistics meaning is a major industrial level commercial process. It requires a large transport infrastructure to concentrate commercial goods at a port that has the size and infrastructure to handle big ships and heavy containers. And it requires the vehicles and starships to be designed to optimally handle those standardized containers. That absolutely exists in Traveller in some form, though that that form looks like can be hard to say since surface to orbit part of the flow is not something we get any details about in Traveller and the standard assumption is those large ships don't land at the downport.
However, I have been talking about Free Traders as a class (whether you mean Type A, Type R, Serenity, The Millenium Falcon, or any other such ship) this entire time and discussing cargo handling on that kind of vessel. They are not designed to fit easily into that containerized trade paradigm. They are independent, they do not operate to a schedule, they are too small for any economies of scale, and all the examples we have are horizontal loading, which is not great for big awkward containers.
The primary characteristic that makes a good free trader is being cheap (aka small) and able to go anywhere (streamlined, again small). They need to be able to operate at a class E starport or just land at some winery in the boondocks to bypass the Tukera stranglehold on the port. So it makes no sense for them operating as container ships. Their raison d'etre is going places that probably don't have the facilities to handle them. No matter how disposable you think containers are, no one is sending a containerized ship to the Port of Humboldt Bay. It can't process them.
General Cargo still exists as a shipping class even today because there are places that get trade that can't handle containers and because there are goods that are not ideal for containerization. Free Traders thrive on that. That is what they exist to do. It is why they are designed the way they are.
Traveller is a game. It wants plucky free traders in the stars to be a thing, unlikely as that seems. It tries super super hard to avoid post scarcity despite miniaturized fusion power (Fusion+), unlimited reactionless in system transport, advanced robots, and fabricators. The important thing is to design this imaginary trade system to be fun for adventuring. What that means to your table is going to be different than it is at mine.
I think that anti grav so controllable it's TK is not good for adventuring (because of the implications for PCs boarding or being boarded).
I think that exo-loaders are cool even though they (like all mechs) are actually stupid compared to regular vehicles.
I think that a cargo bay full of all kinds of assorted goods is more fun to have a fight in than one with wall to wall containers.
I think that the PCs being able to land and trade with some outback village is more fun than being limited to a proper container port.
I think the purpose of the trade rules and the free trader designs is to get the PCs into adventures, not to be optimal for corporate efficiency.
If you come in with different assumptions about what is fun you absolutely should make different decisions about how free traders work in your game. That is, in fact, the point of the ambiguity that some people hate so much.
Like you I don't see free traders as being equivalent to the bigger container ships that will haul the bulk of cargo in Imperial space. Free traders would carry much smaller containers in the 3-5dton class, or even just palletized cargo - though that might be a bit of a stretch even for them. Containerization works great for cargo movement and also allows for transhipment without all the hassle of tracking a single pallet. Though as you point out, free traders would be able to deliver cargo directly to smaller ports that bigger container ships would never be able to do, thus they would have the ability to do so, though it seems unlikely.
I do think, however, that free traders and smaller ships would still operate on somewhat of a fixed schedule. We have to remember that in the Traveller universe schedules are, at best, guidelines. With the vagaries of jump space it's simply impossible to have exact schedules unless you build in a great deal of buffer time. And the farther you go the more inaccurate the schedules get due to increasing random travel times. In this case it's also more likely to adopt ye olde schedules of freighters, or even sailing ships, whereby you have a generalized time frame for when you expect the ships to arrive and depart. Which is easily handled by freight forwarders knowing which ships generally ply which routes, and shippers knowing that they would need to have cargos ready to go or even already at the local port or orbital warehouse waiting for the ships when they arrive. That means ships can spend less time in port looking for cargos since they are already on the board waiting to be picked up by a certified hauler (or purchased on spec - though I have to wonder just how much cargo is going to move that way... seems terribly inefficient and risky).
Ambiguity is fine, up to a point. After all, why buy a game system that defines very little? We are paying for a game framework that is mostly already pre-defined. Otherwise too much ambiguity results in a waste of gaming dollars. Most of us here have fertile enough imaginations to create this stuff ourselves - but its much easier to buy something with most of the heavy lifting done.