Empty seed containers are a nuisance: You keep acquiring them on a regular basis (especially while evolving your crops), they tend to not stack despite being functionally completely identical once emptied, and the only way to dispose of them properly - the waste baskets - have a cumbersome interface.
How about implementing one (or more) of the following:
(a) Simply have seed containers disappear once they're emtpied.
(b) Replace them with a different, property-less item, "empty seed container", once they're emptied, to make them stack, so the need to dispose of them in a timely fashion is not as severe.
(c) Improve the waste basket user experience to make disposal of empty seed containers less of a hassle.
(d) Add a slot to the Seed Production Machine interface to recycle empty (or obsolete) seed containers.