“Operation of the scholarly system”

This means:

how the scholarly system actually functions in practice.

For example, you might discover:

Scholars from prestigious universities receive substantially more citations even when publication volume and field are similar.

That raises a question:

Why?

Perhaps prestige affects:

• visibility;
• networking;
• conference invitations;
• editorial attention;
• collaboration;
• students' awareness;
• citation behavior.

You are no longer merely describing:

“Professor X has many citations.”

You are investigating:

What mechanisms cause some scholarly work to become more visible and influential than other comparable work?

That is what I mean by studying the operation of the scholarly system.