I checked the bugs. It's impossible to vote for them because they were all marked by you as "not a bug." But I would disagree. (And I spent quite a bit of time looking all this up.) I did post on the one bug report, a shorter version of what I'm posting here, since those were basically closed.
https://en.boardgamearena.com/#!bug?id=5186
https://en.boardgamearena.com/#!bug?id=6748
I cannot open the links provided in those two reports.
https://en.boardgamearena.com/#!bug?id=8376
The link in this one I was able to open, which leads to exactly what someone else linked to. This is a set of Rio Grande rules c.2002/2011, which is a re-write of the original with the expansion added on. I have the original 2002 rules, and the only expansion rules I have are here:
http://riograndegames.com/games.html?id=159. This is not very "polished," but I read somewhere that the expansion was originally put out in some German magazine, and that might be the rules that went with it. These are the rules I referred to myself when I posted above.
But I went through the link you provided in that last bug report. Under Harbor (pg. 10) it says "Each time, during the captain phase, the owner of an occupied harbor
loads goods on a cargo ship, he earns one extra VP." (stress mine) The example that follows does not mention "types" of goods at all, and while it provides an example combined with Wharf, there is no example combined with Small Wharf. It does
not say what you quoted in the bug reports. I also started at the top and did a search for "harbor" to see where there might be extra information. I found none. All other references are just minor, not related things.
Your quote of the Harbor included the phrase "good type." I did a search for that as well, and the only references are for the warehouses. Nothing related to the harbor, or to either of the wharfs, including the examples. (Literally, when I hit "next" it just jumped back and forth between the small and large warehouses.)
I also searched Lighthouse - you quoted that as saying "type of good." I can't find that either. It says it's "similar" to the Harbor, except it's doubloons instead of VPs. Nothing about good types.
In other words, what you quoted simply does not exist in the rules you linked to. If I had to guess, I would just say maybe the rules changed somewhere along the way, as we know happens. But the expansion rules I have seem old, so not sure exactly when they would have changed. (I am not, of course, saying you made that up. But I am pretty curious where that came from, when I followed your link and it doesn't exist.)
In the end, I simply can't find your version of those rules anywhere.
The only thing I could find on BGG was this:
https://www.boardgamegeek.com/article/9664421#9664421. Unfortunately it's just a comment from one guy, but no one refuted him. And I did a search on there as well, looked through all references, and see no other questions about the Small Wharf, meaning... no one is asking. I usually take rules as literally as possible (and am right 98% of the time - yes, I made that % up

), and my interpretation was "per shipment" meaning the entire shipment. If a shipping line loaded shipments for various companies, the company would be making "a shipment" or have "a load" regardless of how many different items were in the shipment. If they had, say, 4 cartons of one product, 2 cartons of another, and 5 cartons of another, I would consider it all one load going onto the ship.
That said, if you changed the rules now, it might freak out some people who are used to it the way it is.