Rewriting the Suggestion because after rereading it I did a horrible idea explaining it and confused too many people.
Long duration boxes that allow for multiple harvests of a crop should store their harvests and allow for one collection at the end of the boxes life as opposed to what it is now where you have to babysit the box and come back every X hours if you want to utilize longer duration boxes/short grow time mushrooms.
With the idea above, when placing a box players should be able to queue multiple types of mushrooms/substrates that will grow in the order that they are placed in the box (assuming they're withing the boxes duration limit).
The idea is basically to make it a bit more friendly to the players time.