When you export semi-products from City X to City Y, you'd think they would go through the industrial port right? But they don't ... ALL exports/imports actually go through the nearest Commercial Port.
It would be really nice if industrial ports would function as hubs for the actual industrial import/export of goods so you can build your industry around them. I'd settle with it if the game checked for which ever (industrial/commercial) port was closest and used that one. (although limiting type of goods per port is more interesting as a gameplay feature wise so I would recommend that if possible as it also makes intuitive sense)
Another thing I noticed, if you don't have any commercial ports for whatever reason (only possible using a script) you can still export/import from other cities (which is good) however all transactions go through coordinates 0,0 (the top north of the map) which is a bit of a funny quirky effect lol. Meaning the more north you build on the map the cheaper it is too transport to/from cities
Finally Truck Transport costs across a city map are ... quite staggering and a little too much in my opinion. Especially for some goods they can be huge. Meaning that often times you'll be paying a lot more for truck costs to and from a company/seaport than from actual seaport charges for going across the entire world map. The truck cost component could probably do with a nerf of 50% of the costs (though a script command which allow you to set truck/ship costs multiplier separately would be absolutely amazing and a superior fix/feature!). Truck costs are truly massively high right now (which can be good or bad depending on what you prefer gameplay wise). The effect is that it's overly powerful to build your industry around a commercial port to keep transport costs as low as possible and it means that hugging a seaport is overly important in determining freight costs across all cities in-game. I mean it's not a game breaking problem but it's just something I noticed that has a big impact. You absolutely don't want anything to travel far across the city maps because the costs will skyrocket, whereas anything that is built close to a seaport is a little too competitive across cities because of this effect.