It's both a positive and a negative depending on how you use it.
It will clone all the events, etc, however some of the triggers might be copied as well and cause unexpected side effects. So button to open up a pop up, when cloned, will open up the same popup as it's original.
A deep copy is also more resource intensive, so if you deep clone a whole page, it might take a while on slower machines. That's why this is an option.
I usually avoid the deep copy, and try to just clone a template and then enhance it with the events and data I need.
Try sticking your form outside of a jQuery Mobile page(so it's not enhanced), then clone it into the page you want and enhance it.
I haven't really spent any time looking at your particular use case, sorry, so I can't advise more. Please contact me if you need more specific help than this.