Now that macOS 10.12.4 ist out: Is it reasonable to update to Sierra or are the 2 reported shortcomings
- Flickering while editing
- Problems with PDF notes
still there?
Still there. The upcoming version 2.9.11 will include additional workarounds for Sierra. However, as long as Apple releases security & Safari updates for El Capitan, there’s actually no compelling reason to upgrade right now.
That’s the critical piece of information I was looking for - putting Sierra on the back burner again 
. Thank you, Christian!
This is the first time I have been burned on a macOS/OSX update. 
I popped up a comment on a different thread over in DTTG2 - since it is partially related to iOS, given that the annotation notes were created there - but the problem manifests in DTPO, where those annotation notes are now more difficult to view.
So another vote to wait if you can…