I know this has been mentioned before and the authors have stated that this is intended behavior, but I still have some questions about this topic, so please bear with me.
In #1376 the devs said the reason for not enabling seconday seed from mystical aggriculture is because of croptopia right click duplicating the seed, but I noticed that in #745 a new right click to harvest function was added using a Kubejs script and MA seed drops were reenabled, but then it was again disabled again. I have tried enabling it on my singleplayer world and it works fine without duping the seed, so I think in the current state enabling MA extra seeds should be fine, and without it MA progression slows down to a crawl and is really painful, especially when you want a lot of seeds for mass production.
At least if harvesting directly to get extra seeds is a no-go, give us some other means to produce more seeds, like thermal expansion phytogenic insolator maybe?

The goal is that you automate crafting more seeds, rather than just getting free extras. We do not plan to change this at this time.