My use of DT has evolved over the years, so I don’t think I would scrap my current setup. Probably the biggest changes I’ve been through is having one huge (too large) database, then too many small databases, and now what I think are the Goldilocks databases.
Nearly all my resources are stored in the file system and indexed from DT. This allows access from programs like MATLAB, Finder, etc.
Some resources (reference PDFs) are indexed from two different databases. One includes things like presentations for journal club so I can use the magic hat to find related references. The other indexes the new zettelkasten I’ve started (using The Archive), and also indexes the PDFs. Again, the magic hat should provide some serendipitous insights as it considers my notes (zettels), and the PDFs and their references.
I’ve become more flexible in general app use, and no longer try to find the One True Way to do things (as quorm alluded too). For some things, a “workflow” is just overkill, whereas for others, multiple steps, some of which might even be redundant (notes in Agenda and nearly identical and linked items in Things3) can lead to better understanding of the project, its component steps, and even new insights into the work itself.
This post by @anon41602260 was very helpful in this regard. 