I have fixed Color Actions so that the targeting checkboxes apply to "by hetero" etc. and not just the simple coloring buttons.  The fixed version will be available in tomorrow's daily build.

We have a ticket open for executing custom commands after models open (#4748) and I've added you to the recipient list for that.  In the interim, I wrote some simple Python code to execute "lighting soft" after any model is opened.  I attached the file below, and if you add "open wherever-you-put-the-attached-file" to the commands that ChimeraX executes at startup then you should have the soft lighting you like.