Plant boxes sound fine. It actually means you can integrate crafting into the farming segments and would look nicer than an open plot of soil just lying out.
Maybe sprinklers can be unlocked later in game to allow the player to farm and it gives the work bench some importance in the farming area. I however personally don't feel farming is a necessity. In fact it doesn't make much sense owning a workshop and farming. There's plenty of farming sims out there, so you shouldn't feel it's mandatory for it to be implemented.
Maybe even using the assembly station to make a greenhouse and having a separate "map" to do the farm work. This would save space for the your work stations, and would avoid complains of farming plots taking up to much space (though the screenshots make it look like if you use to make spots, it's the players own fault haha)
I feel the twigs and stones on the ground shouldn't cost energy at all. It would allow the player to still be productive - even if they have no energy - and if you are implemented a farm system that will take up more stamina, then you may have to make a few work arounds to try balance out stamina more. Once stamina hits 0, there's really no point in doing anything else except sleep which makes people skip days. So adding a no stamina thing to small gather-ables on the ground would help be productive regardless of energy.
Hiring a farmhand to look after them might help as well. Having an off-location for your crops (maybe you can buy a ruined greenhouse and similar to how you repaired your house, you can use glass/metal pipes to restore the building and use it to grow crops) it becomes optional then and doesn't take up work station areas. Paying someone to look after your crops would include an optional management system too, so you can save stamina but it'll cost you a wage essentially. Of course, this can be later content and not available at the start to avoid being OP early in game.