Good morning Nacin--no, you did not misunderstand.
The misunderstanding was mine, totally.
The surprise on my part was that the .zip file showed up at all in the media gallery. This had not happened before, and I *THINK* it may be due to the fact that WordPress no longer uses blogs.dir.
In 3.4, I had accidently loaded "duplicate" test plugins, and had received the same error message, but I never saw those duplicate plugins show up in the media gallery. At the time, I had assumed that WordPress was simply rejecting them, but perhaps it was throwing the duplicates into the blogs.dir folder.
My concern is that I will have multiple users, most of whom do not have experience with WordPress (not that I have that much experience) who will also be authorized to activate plugins. When they do, and if they accidently load a plugin twice, as I have, then anyone who has the ability to edit a page will have access to those .zip files--and very well may, because the icon looks like a picture of a box--a cute "graphic" they could put in their page. (I tested yesterday as editor). My understanding is that because images are attached to parent posts/pages, I can't restrict access to images unless I also restrict access to posts/pages, and that's just not going to happen. This is my problem, of course, but it is a major concern, as I expect multiple users, including possibly some students, to be maintaining these pages.
It's not specifically the access to the plugin that concerns me, it's the fact that the attachment file took me all the way to my folders inside the site.
Ok, here's where I REALLY make a fool of myself, because I'm not a programmer. I'm just a "learn-as-you-go" kind of person.
I don't *THINK* it's a cookie thing, as I was able to view the plugin in the media gallery across multiple browsers.
It MAY be a session thing, because after shutting down the computer overnight, I will no longer see the .zip file. BUT, significantly, closing the browswer is not enough to make the view disappear.
Install a plugin.
Install the exact same plugin again, get the error message that install failed.
Check the media gallery.
You'll see the .zip file.
When I loaded the icon into the page, it provided a link by which anyone could get into my folder system.
I've got screen shots for you, for further clarification of what I'm talking about.
Right now, on the test site, on the home menu, I have a link "Media Gallery File Types"...more screen shots are there.
Again, thank you for EVERYTHING you and the team do. I am just in awe. Thank you so much to all of you, and what you give to us with this amazing open-source platform.