In terms of material cost building efficiency, 3x5 is the most efficient. It has the highest ratio of farmland to multifarm blocks. For early-to-mid game, those multifarm blocks are expensive.
In terms of operating efficiency, I have no idea. They consume so little power, water, dirt, and fertilizer, that I don't notice or don't really care. Note that in Unleashed, you can convert MFR brown Fertlizer from a Composter into Forestry blue Fertilizer at a 1:1 ratio using normal crafting. I have a 2 MJ/t cyclic assembler to immediately convert MFR brown to Forestry blue and than I can use that everywhere. The MFR fertilizer, Forestry MultiFarm, and Forestry Fermenter all take the blue.
Mid-to-late game, it's easier to craft and setup 5x5 farms. Most of the work (time spent) is in the building and piping. Might as well go max. size when copper, tin, redstone, and gold are no longer an issue.
As far as top hatches go, I go 5x5 and put 2 hatches in the middle 3x3 area of the top. I plop an Item Tesseract straight down on them and have never had a problem with crops trying to occupy the same space. I use 1 Tesseract channel for fertilizer and the other for dirt. You will have "head of line" blocking as I discovered if you try to share a single Tesseract or Tesseract channel for dirt + fertilizer.
Once I have my farms setup, they are mostly "set and forget". The biggest ongoing concern is server load. I try not to build more than 3 and have been trying to "get by" with just 1 these days just for the challenge of it.