Why are photos added to library when they should not

My main organization of photos is a folder that is accessed by Lightroom. Photos taken by my iPhone are added to my iCloud library. Every few weeks, I export them, reimport with Lightroom and then delete from Photos. After deciding what to keep, etc, I import them back to Photos, but as referenced pictures. I've noticed some strange happenings in that some of these re-imported referenced photos are being added to the library in Photos instead of staying as referenced photos. Today, I exported all my December photos to my iMac desktop. I imported to Lightroom by moving them to a specific folder on my iMac HDD. I then went to my iCloud web page, selected all but 12 photos and deleted them. I checked Photos and indeed the pics were gone. I checked my iPhone to see them gone and then my iPad. All but a few stray pics were gone from that device (don't understand my some that had been deleted from iCloud were still on iPad) I deleted those stray pics so the ALL Photos on my devices and iMac Photos showed the same thing, just 12 photos. The following are my Photos preference settings:

My devices have these settings (iPhone also has upload burst photos selected):

After all this was checked and rechecked, I imported my Dec. pics into Photos as referenced photos, yet more than half of the referenced images were imported as photos added to Photos Library. I have a smart album that IDs pics added to the library instead of referenced photos. Even a few were duplicates of the original 12 I had saved to my Photos library at the beginning of this whole experiment. These photos that were added to Photos library are now also on my devices as well as when I check my iCloud web page. How do I keep pics that should be referenced photos from being added as if they are being uploaded? Some of the "uploaded photos" are in a shared file. Would this affect what is happening?