I'm not sure I fully understand, but if by 'not a data silo' you mean you're ok with having an application to view these things, but prefer that they be stored

I'm not sure I fully understand, but if by 'not a data silo' you mean you're ok with having an application to view these things, but prefer that they be stored as real files, rather than a flat database, I strongly recommend EagleFiler. No one of its features is very shiny or mindblowing as the NLP of DEVONthink, for instance, but it's very well thought out and efficient. In particular I think it has the best 'capture' function for taking the frontmost document from the current application and saving it to the EF database (which consists of an index file as well as a regular Finder-friendly file hierarchy)