Does scientific experience matter for a funded PhD application?
From personal experience, and this is not always the case, publications matter and they matter because they show prior research which helps in situations of lower grades. 

However, do be prepared to receive questions in either the interview phase or via email when discussing with the university you will be applying to on why you are leaving in your last year. If your current advisor is in knowledge of your current situation and is willing to recommend you then this may not be a problem at the end.

Hope this helps...