The initial model colors are defined in chimerax.atomic.colors as a list named atomic_color_names.  That list is:

["tan", "sky blue", "plum", "light green", "salmon", "light gray", "deep pink", "gold", "dodger blue", "purple"]

You can use Python code to replace that list.  I have attached a Python file (start_colors.py) that replaces that list with ["khaki", "purple", "dodger blue"].  You could obviously edit the code to put in any color list you want.  Then you could put "open start_colors.py" in the list of commands that ChimeraX executes at startup (under Preferences/Settings→Startup) to have them always apply.  Just so you know, if you have N colors in the list, then the first N model IDs will get those colors.  For models with IDs higher than that, ChimeraX will try to use a color that contrasts with the colors in the list, the background color, and the selection-outline color (green).