Ok, I did not fully understand what you were trying to do.  I will agree, that Quickbooks is not the vehicle for this.  As was mentioned, it might be possible using the Customer and Job, but that it not a clean answer.  Industry accomplishes this by having 2 sets of books and that is the method that I use also.  Industry will have one set of books for tax purposes (set up to minimize taxes in all ways allowable under the tax code) and a second set to accurate reflect management of the company.

I use the old Mapshot's program EasiSuites for my management and costing function.  It is easy to allocate cost down the field level with it using my Agleader Logs as the input.  The newer Mapshot's offering AgStudio is supposed to have this ability in the future, but it is not there yet.  And, I am getting frustrated at the delays. SMS has a very elementary capability of doing what you want, but I would not recommend it.  Farmworks is capable of this, but like you, I do not like their accounting functions either.

I suspect that there are other Ag specific accounting programs that can do this, but I have not found one that was fully capable.  Flagship may have an offering that can do this with Quickbooks, but I am not familiar with their products.

Trying to keep multiple sets of books in one file (essentially what you are trying to do) is not what Quickbooks was set up for.  For tax purposes you want to accelerate expenses as much as is allowable.  LIFO for inventory management, accelerated depreciation, etc.  For management accounting you want to depreciate over the useful life of the asset.  You want to value inventory at average or actually value.