The "Add from Server" plugin carries a big "not updated in 2 years, may no longer be supported" notice...
The size of that notice does grab one's attention, and I also do take note of those. However, that particular plugin worked fine for me just a few days ago and its Changelog does say this:
= 3.2.0.3 =
* PHP 5.4 compatibility
* Special characters in URL fixes
http-level caching behaving strangely, or inefficiently, if it has to cache two urls which are actually the same file
I know nothing about that kind of thing.
wp code that creates thumbnails crashes/misbehave if they already exist
I do know 'Add From Server' just reports "File not added" and does nothing else whenever the registration of a selected upload already exists in the targeted database, but I think your point there concerning what WordPress might or might not do when it discovers the thumbnails already exist might be a valid concern.
wp code of the media library crashes/misbehave when you open the media library, and there are files on disk, never registered in its own database (because uploaded the first time, by another blog, that is registered in another database)
Maybe I am wrong in believing "extras" are simply ignored.
(of course, I will just go ahead, set up everything, see what happens and report...[after] asking and studying, 5 minutes at a time)
I do the same. Just be certain complete backups all around is the final preparatory step!