That thread is ancient. If you want to delete empty folders, you probably don't need external commands for that. Not sure what you're actually trying to do, though.
The script can do that itself without requiring an external exe.
The Opus Delete command has a FAILNOTEMPTY argument which lets you tell it to delete something you think is empty while it will do nothing if it turns out that isn't the case. (Must be combined with NORECYCLE).
Scripts can enumerate folder content to find all folders or all empty folders, or whatever is needed. An example that lists everything under C:\ is included in the button editor's default example script.
But if you do want to use rmempty.exe instead, and you want to make it part of your Opus config, then in or below /dopusdata/User Data is the correct place to put your own files that will be included in config backups. (Paste the path into the location bar and push return to locate the appropriate directory for your system/username/etc.)