I appreciate having other inputs, I think it’s important to refine the idea. Overall, having pure Pandoc + literature note linking as explained in the other FR would satisfy 95% of my needs. Having the possibility to complement the bibliography by hand in the file itself would be great, but not imperative. However, I am not sure to see why it would be hard. And sorry about the tone, I got a bit irritated because I had the impression to explain several times the same thing, especially that I want to avoid as many actions as possible with Zotero because it is SO slow and I am already loosing so much time with this.
Indeed, you can have a reference section at the end of the markdown file with a few references not present in the bibliography file. These items could be formatted as:
[@notinbib]: Smith. “An amazing work”.
and I can use
[@notinbib] to cite in the text, along with any other item present in the bibtex file., say
[@inbib]. Now for the preview / export, Pandoc is first called to generate the bibliography from the bibtex file as usual, and it inserts it in the reference section (let’s say that there are 17 such items). Then we process by hand the remaining citation, replacing
[@notinbib] by  in the text, and then append to the Pandoc-generated list all remaining items. Obviously, this works well for number-based citations, less for name-based citation, but I am sure we can come up with some heuristics/convention.
Also let me re-say a motivation for this: someone may not want to use a reference management software and just cite a few things in some notes, in which case having a simpler system may be appreciated.
I admit it starts to be specialized, so I could imagine this being done by a plugging and not in Obsidian’s core itself (which would process online pure Pandoc, following @WhiteNoise suggestion). The only thing is that the bibliography generation should allow for a way to intervene and reprocess/add references to the list with plugins.
Thanks for the suggestions. Now I am using a collection “Obsidian” where I am moving only what I may use in Obsidian. The only problem is that I have to think in advance what I will likely write on, and this adds some micro-management (moreover, because of the lag problem I mentioned, moving one item blocks Zotero for a few seconds, so it’s painful to move several documents one after this other). I had not thought of using two profiles: I have to think about it, although I fear that it would require too much shifting.