Whether the application is needed or not, it depends on the particular office and also on the urgency of the requirement. There have been cases where for the origin requirement the application part was waved off. However, 99% of the time companies do need a formal application database, so you have to submit the application.
The only difference is what's the order in which these things happen. So, either of two things can happen, when you are going with the referral. The first option is - you have been referred by someone in the company just with the help of your CV. The recruiter goes to the CV and the recruiter reaches you with the links, if your application and CV are impressive, why don't you put a formal application. So, the process starts from there.
The other option, the person who is referring to you, he himself says: "Why don't you go on the general website and apply". and once you have applied, let me know whatever the application reference numbers, I will follow up with the recruiter.
Either of these things can happen, you should get it clarified with the person that is referring you on how it is going to happen.
In anyways, 2 important stakeholders here:
1) the person who is going to refer you
So be in close contact with them and don't take any steps without them knowing.