I posted about this elsewhere in the forums because I thought it might be a bug/mod conflict, and I found that, as mentioned above, some of the plots are made in a different way than SS1 in order to make things work in a more streamlined, less data-intensive way. The base SS2 agri. plots were made in a way that the actual crops on the plot are static, so they will never be harvestable. I do find some food items in my workbench, as well as some things from my industrial plots. I have IDEK's Logistic station installed, so my workshops are pretty clean. Now I can track what my settlements are actually producing for me because they will be the only things in my workhop's inventory. Whenever I travel to a settlement, I check the workshop to see what I've accrued, then dump it all into my logistics locker so every settlement has access to them.
I am, however, running into some weird calculation problems with my settlements' internal resources that show wildly varying numbers between settlements, and absurdly large negative numbers (-2million wood, for example) even though I make sure to have one of each type of industrial plot; scrap, rare, building material, etc.. in each settlement that has settlers in it. Regardless of what I build, nothing seems to be leveling out my internal resource stockpile, and I'm having to pay the daily costs for my plots by hand. I think I've gotten to a point that my plots are so interwoven and reliant on each other that when one fails, they all fail and I haven't found a way to fix it yet.