Further, while land value tax would reduce the average tax burden on the average farmer, it would change the incentives because it would make passively holding onto land less valuable of an activity on the margin even if there's a net savings to the average farmer.
I'm not a fan of factory farming either, but the point you're missing is that the kind of agricultural strategy you and I don't like optimizes NOT for highest yield per acre, but highest yield per dollar of input.
Efficiency is not mono-dimensional, it's not about "more efficiency" it's about "more efficient AT WHAT." And what industrial farming is efficient at is not using money and not using human labor. One of the chief ways it does this is externalizing most of its costs (pesticides, herbicides, runoff, erosion, antibiotics, etc), and grabbing up more land to make up for its lower per-acre efficiency.
Well, of course, but surely the comparison is with regard to total tax receipts.
The reality is that it’s a highly regressive tax. Taxes shouldn’t be a prime driver of economic activity.