Dear Michal,

“is there a right way to edit just the file template.css instead of custom.css? So the template.css will not be recompiled and changes I made to this file will persist? Sometimes I need to do some simple changes (like certain color) and don’t want to create new classes in custom.css just because of this.”

You can add custom css code via template settings -> tab Custom Code -> Custom Css

“For now, I tried to disable the option “Compile LESS to CSS” in Advanced tab, hoping for changes I’ve done in template.css will persist.”
Yes, if you need to edit direct via template.css file so disable compile less to css is good method.