Custom themes support?

I’m looking into creating a custom theme for a frontend view, is there any way i could create custom theme files, without loosing them during updates?

According to the comments in the files any changes done to the template files will be overwritten each time plugin updates\activates, so i was curious if i could create a custom template, which would save each time there was an update for the plugin.

I had an idea of creating a separate folder for the templates and then changing path to the folder in the script file, but i’m afraid these changes to the script could also be overwritten by updates.