This information is tentative. I have been doing some experiments, and here is my best understanding so far: When a bat/btm (Take Command) file is running, you can right click the bar at the top. Then you can configure the properties which includes options, Font, Layout and Colors. You might think Windows stores the properties for each bat file in some secret place, such as the registry, but it does not. It stores only one set of properties, common to all bat/btm files in the registry at Computer\HKEY_CURRENT_USER\Console. If you change the properties, you will change them for all bat/btm files.
If you right click on a *.lnk shortcut, you can change the properties, but these are completely different from the ones you get when you click on a running bat/btm file. For example, they let you change the icon, which often does not take until a reboot.
When a *.lnk shortcut is running, you can right click the bar at the top. Then you can configure the properties which includes options, Font, Layout and Colors. These will be private to just that shortcut. They are stored in the *.lnk file.
Even if you invoke a bat/btm file directly via the bat/btm file, not the shortcut, or if you invoke it via the task scheduler, Windows is clever enough to find the corresponding shortcut on the desktop. How it does that I don’t know.
I think it is necessary to have the same palette defined all your properties, otherwise when you select a colour, the screen will use a colour in some other property, but at the same offset. Even when you do that, often colours mysteriously change all by themselves. It is very frustrating. I think the whole scheme should be redone to give every bat/btm file its own properties, completely independent of any others. Perhaps my new understanding that only *.lnk not bat/btm files have properties may help sort it out.
