Selecting for seediness was something I worried about too. I don’t want a sunflower “gaming” my selection process by producing more but smaller seeds. Even with peppers, where I’m less concerned with seed size, if I accidentally select for seediness plants will end up investing more energy into that and less into other aspects I might prefer. At the same time, I need plants to set seed, so I can’t ignore seed quantity either.
My solution, which I haven’t put into practice yet so take it for what it’s worth, is to cap the number of seeds I save from each plant. I might decide I’m willing to save up to 10 seeds per plant this year. If a plant produces too few seeds, it gets penalized but still has a chance to contribute any other desirable characteristics to the next generation. If it produces more than that, it doesn’t get any extra selection benefit.
The catch is that if I do multiple rounds of harvesting, I’ll need to keep track of what comes from what plant somehow. That’s a record keeping problem I haven’t quite sorted out yet! Maybe I also need to select for uniform ripening on a single plant in order to simplify things for me. (I hadn’t even thought about the amount of detail I need to keep records on as something I could select for until now, but hey why not?)