Hi,
Wow, this is a great reading! And unlike in the "dodgy physics" thread I'm even still somewhat able to keep up with my limited understanding of how a real railroad actually works. So, THANK YOU!!!

This is very enlightening indeed and great food for thought.
Kali, you say you ended up using a value of 45% for the brake% value? This is incidentally only a bit more than what Bill Prieger uses on his MSTS freight cars (100t weight car -- 35kN max brake force). 45% would mean 45kN on a 100t car, about 12kN on an mt one? That looks like some nice "in-between" values in comparison with the MSTS settings.
BTW, empty / loaded weight on freight cars does work, very well so actually.
For example, if you have a boxcar -- set its mass (MT) to say 27t. Then add a cargo component for "bulk freight", enter say 50t in the "capacity" line of the cargo component. And that's how much your car will heavier when ticking the cargo checkbox in the scenario editor. The only difference to the cargo setup of a hopper or other open-top car is that you don't need to attach a shape file and/or animation to the cargo component group in the BIN file.
FWIW, most of the default freight cars (except the open and covered hoppers) do not have this feature. They have an approximated LD weight as basic mass, and do not even have a cargo component at all. So in effect, most of the default cars (tank cars, boxcars, autoracks, coil cars, ...) are always fully loaded -- which is one of the reasons why so many RW trains run around so heavily overpowered. (Another reason is the often quite heavy loads, sometimes even more than their CAPY would allow, see the HSC 70t hopper with a 100t load, for example).
Cheers,
Michael