I'm having exactly the same dilemmas, pot marigolds, leaf beet, buddleia - lots of typical prolific self-seeders which produce tons of branches full of seeds.
Sometimes it seems obvious to me they have to be composted seperately and sometimes I think 'naa, don't bother' and put them in the compost bin.
It's probably not too bad, unless you want to use the soil for sowing seeds which start as puny seedlings in which case lots of weed seedlings are a menace.
I suppose you can buy in compost for that, or bake it in the oven??
I think we had a thread on here a while ago, where someone remembers people baking soil in the fields, in metal containers with fires underneath?