I use both LiquidText and MarginNote 3, depending on context and what I want to do.
I assume when you say “using … MarginNotes3 [sic] (or LiquidNotes [sic]) with DEVONThink [sic]” that you understand that MarginNote is available on iOS and macOS, but LiquidText is iOS-only?
Both applications have strengths and weaknesses. With regard to LiquidText, you can open a document from a DEVONthink database stored in DEVONthink to Go on iOS via Files, annotate the file, and save those annotations to the original in DEVONthink to Go. Though you can add handwritten annotations to the file in LiquidText, those handwritten annotations are not saved to the PDF and need to be exported. This is a weakness – LiquidText supports a subset of standard Adobe-style annotations as well as its own unique annotation figures.
MarginNote, on the other hand, does not open documents via Files and cannot save the annotations back to DEVONthink to Go (or DEVONthink on macOS). MarginNote keeps a copy of the PDF internally to the MarginNote application. The strength of this is that you can associate several PDFs into the same “study” workspace in MarginNote and take notes, creating an outline or mind map of notes, across all those documents. MarginNote also supports capturing all or parts of web pages as part of the “study” workspace, handwritten notes, comments nested inside other comments, links between comments, etc. It is a very robust study/research environment.
(LiquidText also supports multiple documents in the same workspace, but not as robustly as does MarginNote, in my opinion.)
Getting notes out of MarginNote to DEVONthink is a weakness. You have to export the notes as RTFD files, and then import them to DEVONthink. There is no synchronization between MarginNote and DEVONthink. The exported/imported RTFDs are ugly and very poorly formatted. (I don’t think the developer understands how to create well-formatted export files. The app also uses an out of date and poorly formed .mmap MindJet file as an export option – apps that read .mmap files frequently choke on the thing that MarginNote exports. The app can also export OmniOutliner files, but it exports in a dated and somewhat ugly formatted OmniOutliner format.)
I use LiquidText when I want to take reading notes on a single file.
I use MarginNote when I am researching a topic across a library of files and want to have consolidated notes.
Edit: I believe MarginNote is an excellent research tool for note taking and correlating / aggregating across multiple documents. I don’t mean to sell it short. If I were to put my money on one of these apps, or any of their competitors, it will be MarginNote. The developer has made significant strides in the past 12 months updating and upgrading the interface, fixing major instability issues, and adding creative new features. I am hopeful that more improvements, especially with export, are to come.