So I've done some testing and this is what I have discovered:
You can disable the "active" autosave, but when the application or project is closed, the changes are saved automatically. Makes me wonder what happens if the power goes out or if there's a system crash (or if the application crashes). Closing the file tab doesn't save the changes, and when you reopen the file, it will still have the asterisk. Pressing ctrl+s will manually save the file, removing the asterisk.
I have all the checkboxes under "Synchronization" unchecked.
There are no warnings when you try to close a tab, the project, or the application. You can set the "confirm application exit" option, but that is just in general - has nothing to do with modified files.
I'm still going to use PhpStorm over Komodo, but I honestly don't like this behaviour, and it baffles me that this isn't an option that users can control.
EDIT: It appears these changes do not apply to files that have file watchers assigned to them. I currently have a file watcher for my .less files and one for my .js files, and they are automatically saved and compiled as I type.