Hi,
My guess is that after the last Kronos OS update they did not release an updated voice list PDF so the only way to fix this is to manually do it ourselves. I have attached the CSV file I generated out of that voice list PDF, if you are willing to go over it and make changes you can make it an exact match of what you have on your Kronos.
Now, about Combi change. In Global settings, MIDI, there are two options that can be enabled/disabled. Bank Change and Combination Change. I keep the Combination Change disabled to prevent exactly what you said. I did not find a way to make Kronos differentiate from these two when I am sending an init program MIDI event from the app. The program change midi events (MSB/LSB/Patch) I am sending are standard MIDI and Combis are Kronos specific so I am guessing some sysex MIDI events will have to be used here, specific to KRONOS to only change Combis. I am not sure though...
But, there is another way to achieve this. In Edit, in Style Config, there is an option "Map to Program Change". If you enable that and put the MSB/LSB/Patch values that match the combination on your Kronos then when you change the Combi on your Kronos, this Style is automatically selected in the App. So, you can have the Combis saved in the Set List and load them quickly from there. For more "professional use" this is what I recommend also, as you mentioned, for a song to really sound good, you have to use a Combi where instruments/voumes/effects etc are chosen very well. The best way to achieve this is to create the Combi first, put the right instruments, set the effects etc., then make the Style in app, adapted for that Combi.
So, as a summary, each style can "save the Combi" in it but the "calling" should be made the other way around, by changing the Combi on your Kronos. The "Combi Init" message will go into MIDI Arranger and the app will select the Style.
I really hope this will help you. Try it and let me know please.
Thanks.