In terms of the example overlap, I guess imagine you were an apple farmer who was dabbling in genetic modification and your vault contained hundreds if not thousands of relevant notes built intentionally as building blocks to later engineer new methods and directions for experimentation. Would it not potentially be helpful to establish a hierarchy order and stick to it when tagging?
Like, maybe apple remains a solo tag, but perhaps utilizing nesting with process/structure and structure/process tags, the MOC could stay focused and be more easily organized. To me, process/structure would be notes where the processing or processes of apples are of utmost importance but in relation to their structure, like how to squeeze my new franken-apples without damaging the extremely large and delicate mutated seeds. But structure/process may be for notes about why (in terms of processes) the seed shells (structure) to my new apple variation are so soft.
I am not saying nested tags are the answer, I am just imagining possibly further delineating regions while staying broad with tags few and far between. Bottom line is that I guess I would be concerned about broadness and consequently how long it would take to create and maintain these extensive MOCs and whether this maintenance would hold up as the organic iterative process one might hope for.
In terms of the duplicates, I am a little out of my depths with this example, but sticking to apples, perhaps the apple structure note has headings for different apple parts and those headings have a mishmash of embedded notes and headings from other relevant notes about those apple parts. By nature, blocks won’t be too helpful here, so either scrape by with links and effective naming or commit to embedding and adding a commentary embed immediately before or after. I say this because if this isn’t done atomically , the ever important drawn conclusions and connections get lost in the noise. Like, if you solved the soft seed apple squeezing problem and simply write about it beside an embed from that note within a note about your overall apple processing technique, upon later searches it might be overlooked. However, with the effective naming and focused atoms, you are probably all good, so ignore all that, ha.
In terms of the note level filtering, I just saw this post yesterday for the first time, and I have never used Roam, but the idea sounds almost like a live in-note dataview composition workspace: Filtering Everywhere! - #28 by Gaston
I like what you said about notes not being too much longer than a postcard size, but I build MOC/hybrid style mutant notes, and as an aspiring apple farmer, these notes are just as quotable when building new ideas. However, I struggle to effectively and succinctly name these meandering creations, not to mention trying to fit them on a 3 by 5. Of course, this is probably solvable using a more modular approach to MOC construction, but I am an artist, not an engineer, and I hope that I can feel way while designing my ideas, at least in the first pass.
Thanks, for the post and good questions.