there is a big and ongoing discussion around this underway, and lots of work happening - mostly led by @MyriamBoure’s Data Food Consortium project. I have just posted on that thread whether she could post an update
In general yes - we are likely heading towards API and flexible small modules. A step towards this is the work underway in Documenting OFN API and other short-term approaches being taken to enable connection of ofn to other services e.g. via Zapier
I don’t know what Matrix protocol is but I suspect others will. Are you in Slack @Leo239 - the interoperability channel there might also be of interest