There is a new version on https://github.com/VictorErik/Simutrans-Experimental-Ves/tree/passenger-and-mail-classes-gui-combolist (https://github.com/VictorErik/Simutrans-Experimental-Ves/tree/passenger-and-mail-classes-gui-combolist) that you can try.
With it, you can change classes on both passenger and mail compartments.
You should only use the class manager to observe these bugs!!!
If a vehicle has a class 0 its payloads are registered on all classes, creating lots of class entries. Try build a train with class 0 and some other class and you will see it. Same goes for mail.
As you can see from the code, I use the v->get_desc()->get_capacity(i) to find out wether a compartment can be used.
Sorry for offtop, a short question. Will passenger classes replace current "overcapacity" mechanic? I mean "wait for 200% passengers" thing.
Already, there is no "wait for 400%" but simply a button that says "wait for time". The overcrowded mechanics are otherwise the same, also after the classes are implemented.
Have you not tried the nightlies? If not you should try since it's awesome! ;)