Well, honestly, I can't remember specifics of what I was trying to do in TRS2006 10+ years ago. I've lived in 4 different states and had three different jobs since then, it seems like it was another life, hehe.
I can tell you though that every time I've revisited Trainz (all four versions that I own), it's been painful. It always seems like whatever I've tried to do, even when it was just basic, built-in stuff, there were always issues. I really have gotten so frustrated before that I've just said I'm done and quit, but then after a year or two I'd see that there was a new improved version of Trainz available, so I'd buy it hoping it would work better, try again, and would just have more problems.
I decided a few weeks ago to give TS12 a try again, since that's the newest version I have, and it's been kind of a nightmare again. I'm trying to be patient and not give up this time though, but man... I don't know that I have the patience for this.
As for how real RRs operate, well yes, I'm pretty familiar with their operations. There is nothing unrealistic or unprototypical about a mixed freight. It's really common for railroads to receive trains via interchange which contain a random combination of loaded and unloaded cars containing different commodities. And that's really all that I'm trying to simulate: Just a simple yard, with trains coming and going. I'm really not trying to automate much of anything. (The extent of my automation is a single rule for trains arriving on the railroad that says "navigate to yard receiving track." From that point I take over controlling the train.)
If the developers of Trainz had simply decided to save the load data in the consist's data structure then we wouldn't have to resort to all these horrible kludges with cloning cars and hacking their config files, or using user developed rules to try to "instantload" cars as they appear on the railroad. You could just lay out a train in Surveyor, load it up the way you want it, and click "get consist". It would work so beautifully. Instead it's all just silly the way they have it set up: they decided to approach it as if in the real world all trains carry only one product, and are either completely full, or completely empty.
Someone else mentioned just using staging tracks instead of portals. That's a great idea and I'd love to. Seriously, I would really much prefer to do that, it seems like a much more straightforward, easier way to do things. But again, due to the way they designed Trainz, that solution doesn't scale well. If you have those extra trains on the route, it slows things down, even if they're not moving and not visible. :-(
At this point, I've given up on all the funky instantload rules. From everything I've seen, they're either going to limit me to having a train that is fully loaded with the default product for each car, or fully loaded with a product with a specific index (which must be the same for each car.) This will prohibit me from having a mixed freight, so I'll need to clone a few cars and edit what their default loads are. If I'm going to be doing that anyway, I figure I may as well just skip the instantload stuff and change the config files for those cloned cars to be loaded instead of empty by default. I had read elsewhere here in the forum that this is possible. That's what I've been working on today. I've spent most of the afternoon and all of this evening trying to get that to work, but can't. I've finally gotten it to where Trainz at least recognizes my modified config without generating errors or warnings, and it will allow me to place the cloned car on the track. However, it's still empty when I do. :-(
So that's where I'm currently at. Still plugging away for now. Waiting for the point where this starts to be fun and not feel like I'm at work troubleshooting, hehe.