"Stability and security"
Stability of course, it just does not pay to have the server crash

(Even tho it kinda funny when server crash due to the 1999'er Name-Bug)
Security is less an issue, as long as the server itself does not accept uploads nor runs unchecked pk3...
"The latest bug fixes"
That would be fine, but I'd rather see backward compatibility, so that no backporting would be needed. Not all server-owner are in acceptance of the changes that are in svn, like nerfed poison, slower turrets, changed reach of alien asf...
Undeferenced, I'd suggest you ask the owners/admins of the running servers directly, what patches they are running and why they do so.
To my knowledge there is nearly no server running pure svn nor standard packaged server.