Is it safe to duplicate and rename one of the editor Id's to try out an idea and then if it doesn't work out to delete your failed experiment? I've been a little worried about what exactly causes a "dirty mod" .
I never delete or even change the vanilla items, just play with renamed duplicates or new items. Is it safer to do all experimenting in a separate throwaway mod?

Should be no problem deleting one of your own items. Only danger is to delete or rename any default items.
You should delete unused items from the mod anyway.

You can have a disposable mod to play in but sometimes you need to experiment in your "good" mod so you don't have the work of re-creating things just for the experiment. Just have plenty of different back-up versions of your "good" mod and be aware of how to edit the mod details to fix any accidental UDR's or un-wanted modifications of vanilla cells.

You will more than likely end up with your own created assets in the data folder that can be referenced by any mod you choose to include them in, so the boundaries for a test mod and "good" mod can blur a bit. Also scripts you write are included into the data folder and are available to any mod unless you pull them out manually.