I worked in a newspaper in 2007-2008, town of about 5,000 people, no interns but often hired at least one fresh out of college employee. We generally employed one publisher/editor (paper was owned by a different person), one editor/lead reporter, and two general reporters that worked in the office. We also had some reporters from some small outlaying communities (towns with populations in the 100 people range) who would email a column once a week. WE also employed three-four sales staff, a general secretary, and a circulation manager/classifieds. That was what I was in charge of.
We used....Adobe pagemaker I believe it was. It was all on one server, all I had to do when I did the classifieds was open it up on my PC, type in what I needed to do, save and close my pages. Then all the pages were organized by the editor into one big master file that was then saved on the server. A sister paper (owned by the same owner) had the printing press, so that paper would then log in, print off the pages and start the publishing process with the printer. Newspapers were then shipped by truck the 50 or so miles, 4 days a week (M, W,THR, F). Deadline was usually 12:30-1:00 in the afternoon on those days (every day but Tuesday) so that the printer could get them printed and to us by 3:30-4:00 in the afternoon so that they could be delivered that evening. Other papers in our "group" (under the same owner) only printed once or twice a week, but delievered in the late afternoon/early evening.
Also, we were all given keys to the office and could enter and exit as we wanted/needed.
So is it possible then for your MC to enter the office and change the files in that time period? Yes, but s/he would need to cut their story or add to it to fit in the space allotted for the story they are pulling out or irritate the sales staff as well by reorganizing the ads (in our paper, every page except the front page and the 2nd page (the editorial page) had ads.)
Here's what I would suggest, it's a paper that has deadline in the late afternoon for early morning or/by mail delivery. The editor looks at it, saves the master file and leaves for the night. That way the printers can go in at 3 or 4 in the morning or whatever and can pull up the file on their server and start printing. That would give your MC about 12 hours to sneak into the office under cover of night and change things up. That's my experience and suggestions.