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Lightroom won't get confused, because it's only dumping copies into the folder you specify, during the import process. It never touches those files again after creating the copy.
Actually the primary purpose of the "Store a copy of all originals....." is not for backup, but is in fact for quicker (or offline) access when editing or 1:1 zooming any of your images. If the image you are working on is not currently stored locally, Lightroom has to download it from the cloud and it's then stored and accessed locally from the specified location. If the option remains unchecked, those locally stored originals will become eligible for deletion at some subsequent point (which depends on some complex rules). Thus the option is primarily provided to allow the user to have all images always available when working offline, or as a performance aid if using a very slow internet connection.
Lightroom will also monitor the contents of that local folder so that it knows when an original is held locally as well as in the cloud. You can check the Info status of individual images and it will report what type of file (Smart Preview or Original) is currently held locally.
No, the "Store a Copy" only stores originals during the import process... it doesn't pull anything down from the cloud at all, and will not retroactively retrieve anything. It is only your originals copied from the camera or card as you import them.
Actually it does both. When first enabled all the originals that are already in the cloud are downloaded to the specified location. Ongoing imports will also be copied to that location, which includes imports into ANY of the cloud clients...so if importing into Lightroom Desktop the images are copied to that location and then uploaded from there to the cloud. If importing into LrWeb or LrMobile, the images are uploaded from that specific app to the cloud, and then downloaded from the cloud to that specified location when Lightroom Desktop is next launched.
If you want to download a real backup of the photos in the Adobe cloud, you can use the Adobe downloader app - which will pull down all your originals AND the edits (edits are stored as sidecar XMP files). The downloaded files are stored in a date-based hierarchy. This would make a good snapshot of your entire Lightroom catalog:
Adobe Lightroom Downloader App
The downside is, it pulls down everything, and there's no way to tell it "just give me the changes since last time." You get everything, every time.
I'm not recommending use of the Downloader app, as I don't think it's as effective as it could be and might give users the mistaken impression that it's a complete solution. There are too many things that it doesn't appear to download, e.g. in my (extensive) testing ANY metadata added in any of the cloud apps (such as keywords, titles, captions, location data), is NOT included in any downloaded file. That in itself would be a complete showstopper for some people. There are a few other oddities as well.
Ironically, in my testing it did appear that subsequent runs would only download new assets added since the last run, though it was a little inconsistent.
Yes, this is how I understood it worked. If you have a new machine, and set up LR for the first time on that machine, with the "store a copy" option set, LR will download all the originals from the cloud to that location right?
Yes.
Given that's the case, do you have a view on what happens when that location already contains all the originals?
Assuming you have first copied the complete folder hierarchy from your other system, so that it matches what Lightroom on the new system would expect, when you first install Lightroom you of course need to set the two preference options (changing the location from the default first, and then enabling the "Store a copy of all originals" second). Done in that order, when you enable the "Store a copy..." option I would expect Lightroom to first check the new location, where it should find that it already exists. In that event, I believe it will do a verification analysis of the folder to see which files, if any, are still needed to be downloaded. If it's a complete copy, no images should be downloaded.
But as I said earlier, that was from a long-ago test, so I can't guarantee it will work exactly that way. All you can do it try it.
I do view this as a sort of last-resort backup. What happens if Adobe has some sort of catastrophic failure of their cloud system, or a bug that wipes some photos? Not exactly unheard of - there's already been a bug in the iOS app that irretrievable lost photos. Ok, I wouldn't have my edits, but at least I'd have my originals. I guess this does lead on to a broader topic of how to have a complete backup of everything if the cloud storage fails.
I'm sure many users also use that option as a last-resort backup, and there's no harm in doing that if that's all you've got. Adobe's take is that they are responsible for ensuring that your cloud-based images are full backed up, but without specific details it's easy to understand in the modern world why some users need to be more in control on their backups. The example you quoted, ironically, is a vote FOR the cloud, not against it. The only users affected by that bug were those who had NOT used the cloud, thus there was no backup available to them.
But yes, it is a broader topic which is frequently discussed here in the forum. If I was in need of my own backups from the cloud, I would only consider using the Export with Original + Settings method, but doing that on a regular periodic frequency would be a difficult thing to manage. It's OK as an exit strategy, but difficult as a regular backup procedure.
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