Yes, I could do that but it means using an external editor, save the file and upload it to the server for every change.
No, it wouldn't. If you put the file in the templates folder, you can open it and edit directly from PivotX (using the Media browser). And that editor isn't Wysiwyg
I think your idea about checking if the content contains "[[php]]" and turning off Wysiwyg is doable. There is a hook named "entry_edit_beforeedit" which has the entry (array) as input. In that hook you probably could change the text_processing setting for the Smarty $user array. Yes, it's a little bit complicated and not documented. I don't have time to do it myself now.