According to Windows: killing the Zone.Identifier NTFS alternate data stream the Zone.Information is:
The Zone.Identifier NTFS alternate data stream (ADS) is appended to Internet downloads by browsers, and inserted by most decompressors when expanding such downloads.
ZoneID=3 means it was downloaded from Internet zone (as opposed to Local Intranet etc) ....
Have you just tried using iCloud drive on the Mac and the "Files" app on the phone/iPad, with shelves represented by sub-folders?
Apps are opened and marked in Preview on the Mac and in-app markup is allowed in Files.
All changes are synced. Elegant. Free. Baked-in using no extra apps.
You can activate this behavior in iTerm2 by activating the "Look up & data detectors multitouch shortcut. On Force Touch trackpads, by default, that means a force press by default while the cursor is placed over the filename.
You can confirm your settings in System Preferences, by viewing the Trackpad pane.
You may also wish to hold CMD and click on ...
This behaviour still works for me in Mojave: Preview's Toolbar has a highlight icon. When active (the lighter colour seen in the image below), then you can highlight text in the way you describe.
The behaviour you're seeing may be what happens when the highlight icon is not active (the same shade as the other icons).
This is not a solution but still a work around.
Convert the PDF document to an image with File » Export .. Choose PNG as the format and change the resolution as desired.
Open the image file and select the whole image with Edit » Select All (or select just a part of it with the mouse if you wish).
Copy the selection Edit » Copy.
Go back to the document (...
Without purchasing Adobe Acrobat Pro, I couldn't find a way of removing the disabled layers from the PDF so that Preview will not get confused.
I was able to find an alternate solution for my end goal of exporting the PDF as an image.
In Acrobat Reader,
Edit > Take a Snapshot (enable)
⌘-A to select the whole page (now Acrobat copies the image to clipboard)...