Hello J J Weimer,

At one level, you will find apps such as PDFExpert and PDFPen. They
expand the tool sets to the iPad with additional markup options. I
believe that both have been given high regards on this forum.

PDFPen -> https://smilesoftware.com/pdfpen-family/
PDFExpert -> https://pdfexpert.com/ios

Actually, it was reading the recommendations in this forum that had me trying out PDFExpert on my iMac, MacBookAir and iPad. I now have PDFExpert as my general default PDF reader! :)

In terms of using a PDF editor in my workflow, I am after something similar to Highlights where the highlights and notes appear as text and images in a window to the side of the PDF. These notes are linked to the PDF itself and can be imported into other applications. PDFExpert and PDFPen do not have this extra window with the notes appearing as little icon images on the PDF which you have to click to read what they are.

In this regard, your suggestion of LiquidText and MarginNote seems inline with my needs. You wrote ...

Going further, you will find apps such as LiquidText and MarginNote.
They include their own internal options to extract the annotations to a
side sheet and organize them for review. The downside of these two is
that the annotations they create are not always compliant with other PDF
editors.

LiquidText -> https://www.liquidtext.net
MarginNote -> https://www.marginnote.com

At first, I was excited by the features of these two applications. But their weakness comes from the point you raised about them not being compliant with other PDF editors. They do not to be compliant with other PDF editors as such, but I need the highlights and notes I made in the application export to another application.

In my search for an application for the iPad I came across Flexcil https://www.flexcil.com . Have you tried this application?

You may find that MarginNote (or LiquidText), with their additional
study sheet approach, will provide a framework that you can use directly
without having to export the annotations to other apps. In this regard,
I particularly appreciate the approach in MarginNote to be able to put
tags on annotations.

I need to investigate this study sheet approach further in the applications MarginNote (both on macOS and iOS) and LiquidText (iOS only, unfortunately). I need to see if they can help bring together a lot of different quotes and notes made on different PDFs into themes and concepts.
I would be sort of following a Grounded Theory approach to the analysis of the literature. Mm ...

Personally, I use PDFExpert to do markup that must be compliant with the
rest of the world (e.g. when I have to markup documents that are to be
sent to the Windows community). I also appreciate the ability in
PDFExpert to be able to access multiple cloud services (Google Personal
+ Google Work + Dropbox Personal + Dropbox Work + ...). I use MarginNote
to make annotations that I want to tag for some reason or another (e.g.
when I grade documents, I can mark tags such as "incorrect",
"inadequate", or "improper" to denote different levels of mistakes). I
do not use the collect or study aspects of MarginNote even though these
two additional aspects are touted as the main reason for MarginNote to
be used (markup + collect + study). I do not appreciate the limitations
and general instabilities that MarginNote has in syncing only with
iCloud (and have given it a low review on the App Store for this
reason).

Tagging would be one way I could do this. I will try and find out some more.

If I have sparked your mind for other suggestions or ways of doing things, they would be most welcome! :)