It would be good if Industrial Hemp (from IE) and Flax (from Blue Power) can yield a seed as a secondary drop, since - especially with hemp - the seed is more important item than the primary yield.

I think to same thing like poisonous potato for potato and icy needle for witchery snowbell.

This has been requested before, however it doesn't fit into how agricraft works, It's possible to set up an automated system to have one crop spread to 4 neighbours and then harvest the newly spread crop (plant + crop sticks) and apply a new set of crossing crops.
You could even just use autonomous activators to use a rake and crop sticks to farm seeds.
Options enough.

Yep, but as your support spread over all farming mods, there will be no easy way to automatically farm stuff by breaking the whole block (crop+plant).

AA can work - if you have any block like this, but cannot work in a ThermalExpansion-less world, especially in magic-focused worlds (flax seeds are for make paint buckets so they're purely asthetical and no industrial style included here).

i think there must be a config option or something for industrial hemp seeds since with disabled vanilla farming you cant farm industrial hemp seeds unless doing it manualy with the clipper or cross breeding which is a pain

Edit: for now my workaround will be a shapeless recipe to craft 1 industrial hemp fiber into 1 industrial hemp seed

For BluePower, check this, for IE, it has only this but maybe it would not help for you. I think both plant need a bit better chances than poisonous potato yields.

Another idea is swapping the product - however, as the main product will become a seed, I have no idea how can it affect the progression. Anyway, the seed should be yielded.