Yes vibration is used to in some seeders to align seeds into 1 by 1 rows and does work no detectable effect on germination rates. Notice the rotation cup in this one that takes 1 seed. This one take major differences in seed size.
By the way round seed counters was first invented as bead counters until one day someone dropped seed in them and it worked.
Most things you can think of in seeders has been done by different groups. Most come back to the same basic core idea hole of some for to set size volume of seed to drop. At the top of a bead/seed counter is a shelf just wide enough for the seed/bead if it too wide it falls back into the hopper that is how they are adjustable. Again its a fixed size hole solution with different transport system. Some was this can be less damaging.
Key thing with the vibration is keep it gentle. Also do remember vibration + bolts can equal undone bolts so how ever you do adjustment has to be tolerant to this some of the cheap bead/seed counters you run into the issue where adjustment ends up locked because adjustment system is not designed well enough.
Josh as soon as you go away from the fix size hole complexity goes up massively. Seeds do stick to each other at times. Add in some vibration and complexity goes up more. Not that I am saying not attempt this just be aware issues and you should be able to make something that works successfully. Using vibration and forgetting to make every bolt holding in the design lockable is a common one.
Yes 3d printed will most likely have to go through smoothing process or the ridges of the 3d printing will give places for the seeds to bind.