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My use of the calibre server has always been pretty basic. It's enabled to run when I have calibre running on my laptop. I really only use it as one of the tests for the browser on my Kobo devices.
I doubt if a service running on a Linux server will be able to tell if a client machine is directly accessing a file on the server. It depends on what locking is done. And that depends on the applications, OSes and file systems involved.
From what I understand of what Kovid has said about the v3 server, what the OP is doing shouldn't work. Or will have problems. The calibre UI is updating the database, independently of the calibre server, and there is a potential for disaster. What the OP is doing sounds like something for calibre v2 and they haven't changed.
And yes, lock files have been a popular way of trying to prevent multiple updates or uses of an application. They can work but everyone (code or people) has always update them appropriately. Otherwise, all you hear in the office is someone searching for someone to remove the lock file. Or trying to find the person who went to lunch without closing the application and now their PC is locked.
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